[gmx-users] Problem with incorrect GB-Polarization Energy Value
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Aug 29 19:55:43 CEST 2012
On 30/08/2012 3:43 AM, jesmin jahan wrote:
> Hi Justin,
> Thanks a lot for your reply. I really appreciate the gromacs_user
> folrun help line.
>
> I see! thats why you are not receiving any attachment!
>
> My goal is to compute only GB-energy. I have computed only GB- energy
> using Amber and Other packages. Now I am using Gromacs to do the same.
>
> As suggested by Mark, I am usually deleting all the bonded terms for
> the topol.top file and also setting the non-bonded parameter values to
> zero in the ffnonbonded.itp file, so that other computations do not
> occur and the timing I get only reports that of GB- Energy.
... which is potentially reasonable only with mdrun -rerun, and IMO not
useful regardless. Timings from a single step of anything are useless
too. One is only interested in the time to compute things on thousands
to millions of these configurations.
> I have done this for different 168 protein molecules and Gromacs is
> performing really well and the energy values are comparable with amber
> and Octree based approach.
>
> However, for CMV, I am getting an energy value which is almost half of
> others. So, to check, now I am not excluding any bonded terms and
> using the original force field files provided in gromacs/share/top
> folder. Still the value for GB-energy is the same as before :-(.
All the energy terms look like garbage. Visualize the output of pdb2gmx
and look for problems, particularly with regard to termini of distinct
protein chains.
Mark
>
> Here is the log file content (without any modification in .top file
> and without the mdrun-rerun command).
>
> Input Parameters:
> integrator = md
> nsteps = 0
> init-step = 0
> ns-type = Grid
> nstlist = 10
> ndelta = 2
> nstcomm = 10
> comm-mode = Linear
> nstlog = 1000
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstcalcenergy = 10
> nstenergy = 100
> nstxtcout = 0
> init-t = 0
> delta-t = 0.001
> xtcprec = 1000
> nkx = 0
> nky = 0
> nkz = 0
> pme-order = 4
> ewald-rtol = 1e-05
> ewald-geometry = 0
> epsilon-surface = 0
> optimize-fft = FALSE
> ePBC = no
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = No
> bPrintNHChains = FALSE
> nsttcouple = -1
> epc = No
> epctype = Isotropic
> nstpcouple = -1
> tau-p = 1
> ref-p (3x3):
> ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress (3x3):
> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> refcoord-scaling = No
> posres-com (3):
> posres-com[0]= 0.00000e+00
> posres-com[1]= 0.00000e+00
> posres-com[2]= 0.00000e+00
> posres-comB (3):
> posres-comB[0]= 0.00000e+00
> posres-comB[1]= 0.00000e+00
> posres-comB[2]= 0.00000e+00
> rlist = 1
> rlistlong = 1
> rtpi = 0.05
> coulombtype = Cut-off
> rcoulomb-switch = 0
> rcoulomb = 1
> vdwtype = Cut-off
> rvdw-switch = 0
> rvdw = 1
> epsilon-r = 1
> epsilon-rf = inf
> tabext = 1
> implicit-solvent = GBSA
> gb-algorithm = HCT
> gb-epsilon-solvent = 80
> nstgbradii = 1
> rgbradii = 1
> gb-saltconc = 0
> gb-obc-alpha = 1
> gb-obc-beta = 0.8
> gb-obc-gamma = 4.85
> gb-dielectric-offset = 0.009
> sa-algorithm = None
> sa-surface-tension = 2.25936
> DispCorr = No
> bSimTemp = FALSE
> free-energy = no
> nwall = 0
> wall-type = 9-3
> wall-atomtype[0] = -1
> wall-atomtype[1] = -1
> wall-density[0] = 0
> wall-density[1] = 0
> wall-ewald-zfac = 3
> pull = no
> rotation = FALSE
> disre = No
> disre-weighting = Conservative
> disre-mixed = FALSE
> dr-fc = 1000
> dr-tau = 0
> nstdisreout = 100
> orires-fc = 0
> orires-tau = 0
> nstorireout = 100
> dihre-fc = 0
> em-stepsize = 0.01
> em-tol = 10
> niter = 20
> fc-stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake-tol = 0.0001
> lincs-order = 4
> lincs-warnangle = 30
> lincs-iter = 1
> bd-fric = 0
> ld-seed = 1993
> cos-accel = 0
> deform (3x3):
> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> adress = FALSE
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 1.5291e+06
> ref-t: 0
> tau-t: 0
> anneal: No
> ann-npoints: 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp-flags[ 0]: 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm-opts:
> ngQM = 0
>
> Initializing Domain Decomposition on 16 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 0.425 nm, GB 1-4 Pol., atoms 24304 24312
> multi-body bonded interactions: 0.425 nm, Proper Dih., atoms 24304 24312
> Minimum cell size due to bonded interactions: 0.467 nm
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 16 cells with a minimum initial size of 0.584 nm
> The maximum allowed number of cells is: X 43 Y 43 Z 43
> Domain decomposition grid 4 x 2 x 2, separate PME nodes 0
> Domain decomposition nodeid 0, coordinates 0 0 0
>
> Detecting CPU-specific acceleration. Present hardware specification:
> Vendor: GenuineIntel
> Brand: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz
> Family: 6 Model: 44 Stepping: 2
> Features: htt sse2 sse4.1 aes rdtscp
> Acceleration most likely to fit this hardware: SSE4.1
> Acceleration selected at Gromacs compile time: None
>
> WARNING! Binary not matching hardware - you are likely losing performance.
>
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw: FALSE
> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
> System total charge: 780.000
> Generated table with 1000 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
>
>
>
> Linking all bonded interactions to atoms
>
> The initial number of communication pulses is: X 1 Y 1 Z 1
> The initial domain decomposition cell size is: X 6.33 nm Y 12.66 nm Z 12.66 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.000 nm
> (the following are initial values, they could change due to box deformation)
> two-body bonded interactions (-rdd) 1.000 nm
> multi-body bonded interactions (-rdd) 1.000 nm
>
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1 Y 1 Z 1
> The minimum size for domain decomposition cells is 1.000 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.16 Y 0.00 Z 0.00
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.000 nm
> two-body bonded interactions (-rdd) 1.000 nm
> multi-body bonded interactions (-rdd) 1.000 nm
>
>
> Making 3D domain decomposition grid 4 x 2 x 2, home cell index 0 0 0
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
> There are: 509700 Atoms
> Charge group distribution at step 0: 31431 30755 30753 31435 33210
> 32021 32023 33214 32024 33215 33217 32028 30752 31434 31432 30756
> Grid: 12 x 20 x 20 cells
> Initial temperature: 0 K
>
> Started mdrun on node 0 Wed Aug 29 09:58:13 2012
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih.GB Polarization
> 2.49688e+06 4.48143e+05 1.23111e+06 1.83801e+04 -2.49498e+06
> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential
> 8.56489e+05 5.21939e+06 3.98993e+05 -8.11154e+06 6.28585e+04
> Kinetic En. Total Energy Temperature Pressure (bar)
> 7.32160e+06 7.38446e+06 1.15177e+03 0.00000e+00
>
> <====== ############### ==>
> <==== A V E R A G E S ====>
> <== ############### ======>
>
> Statistics over 1 steps using 1 frames
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih.GB Polarization
> 2.49688e+06 4.48143e+05 1.23111e+06 1.83801e+04 -2.49498e+06
> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential
> 8.56489e+05 5.21939e+06 3.98993e+05 -8.11154e+06 6.28585e+04
> Kinetic En. Total Energy Temperature Pressure (bar)
> 7.32160e+06 7.38446e+06 1.15177e+03 0.00000e+00
>
> Total Virial (kJ/mol)
> -1.57464e+07 5.62500e-01 -2.12500e+00
> 3.28125e-01 -1.57464e+07 3.25000e+00
> -3.67188e+00 -2.68750e+00 -1.57464e+07
>
> Pressure (bar)
> 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00 0.00000e+00 0.00000e+00
>
> Total Dipole (D)
> 9.76562e-04 0.00000e+00 1.95312e-03
>
>
> M E G A - F L O P S A C C O U N T I N G
>
> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
> NF=No Forces
>
> Computing: M-Number M-Flops % Flops
> -----------------------------------------------------------------------------
> Generalized Born Coulomb 1.626204 78.058 0.3
> GB Coulomb + LJ 73.629096 4491.375 17.3
> Outer nonbonded loop 1.962706 19.627 0.1
> 1,4 nonbonded interactions 1.348860 121.397 0.5
> Born radii (HCT/OBC) 78.053220 14283.739 55.0
> Born force chain rule 78.053220 1170.798 4.5
> NS-Pairs 245.058526 5146.229 19.8
> Reset In Box 0.509700 1.529 0.0
> CG-CoM 1.019400 3.058 0.0
> Bonds 0.514800 30.373 0.1
> Angles 0.934260 156.956 0.6
> Propers 1.742760 399.092 1.5
> Virial 0.510420 9.188 0.0
> Stop-CM 1.019400 10.194 0.0
> Calc-Ekin 1.019400 27.524 0.1
> -----------------------------------------------------------------------------
> Total 25949.137 100.0
> -----------------------------------------------------------------------------
>
>
> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>
> av. #atoms communicated per step for force: 2 x 103046.0
>
>
> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>
> Computing: Nodes Number G-Cycles Seconds %
> -----------------------------------------------------------------------
> Domain decomp. 16 1 2.870 2.0 0.7
> Comm. coord. 16 1 0.943 0.6 0.2
> Neighbor search 16 1 20.102 13.7 5.0
> Force 16 1 132.542 90.4 32.7
> Wait + Comm. F 16 1 2.315 1.6 0.6
> Update 16 1 0.130 0.1 0.0
> Comm. energies 16 1 0.090 0.1 0.0
> Rest 16 246.272 167.9 60.8
> -----------------------------------------------------------------------
> Total 16 405.265 276.3 100.0
> -----------------------------------------------------------------------
>
> Parallel run - timing based on wallclock.
>
> NODE (s) Real (s) (%)
> Time: 8.635 8.635 100.0
> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
> Performance: 8.715 3.005 0.010 2398.708
> Finished mdrun on node 0 Wed Aug 29 09:58:22 2012
>
>
>
>
> Thanks,
> Jesmin
>
> On Wed, Aug 29, 2012 at 1:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>> On 8/29/12 1:06 PM, jesmin jahan wrote:
>>> Dear Justin,
>>>
>>> Thanks for your reply.
>>> Here is the CMV.log file . Please check it.
>>>
>> What you've posted is output from grompp. Note that if you're trying to
>> send attachments, the list rejects them.
>>
>>
>>> Actually, the .pdb file I am using is already minimized and we are
>>> using the same file for amber 11 and Octree based molecular dynamic
>>> package.
>>
>> Something doesn't add up. The energy values were indicative of a completely
>> unphysical system.
>>
>>
>>> I will also do the minimization step to see what happens.
>>>
>>> One thing I also want to mention is when I run
>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr command, I get
>>> following the log.
>>>
>>> NOTE 1 [file mdr.mdp]:
>>> Tumbling and or flying ice-cubes: We are not removing rotation around
>>> center of mass in a non-periodic system. You should probably set
>>> comm_mode = ANGULAR.
>>>
>> For a single-point energy evaluation this probably isn't significant.
>>
>>
>>> NOTE 2 [file mdr.mdp]:
>>> You are using a cut-off for VdW interactions with NVE, for good energy
>>> conservation use vdwtype = Shift (possibly with DispCorr)
>>>
>>>
>>> NOTE 3 [file mdr.mdp]:
>>> You are using a cut-off for electrostatics with NVE, for good energy
>>> conservation use coulombtype = PME-Switch or Reaction-Field-zero
>>>
>>>
>> Finite cutoffs do have a significant outcome of implicit calculations, but
>> if you're doing this to remain consistent with other software, I suppose you
>> have to keep them as they are.
>>
>>
>>> NOTE 4 [file mdr.mdp]:
>>> No SA (non-polar) calculation requested together with GB. Are you sure
>>> this is what you want?
>>>
>>>
>>> Generated 2211 of the 2211 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 0.5
>>> Generated 2211 of the 2211 1-4 parameter combinations
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A2'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B2'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C2'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A3'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B3'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C3'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A4'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B4'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C4'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A5'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B5'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C5'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A6'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B6'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C6'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A7'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B7'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C7'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A8'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B8'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C8'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A9'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B9'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C9'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A10'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B10'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C10'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A11'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B11'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C11'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A12'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B12'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C12'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A13'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B13'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C13'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A14'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B14'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C14'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A15'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B15'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C15'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A16'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B16'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C16'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A17'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B17'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C17'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A18'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B18'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C18'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A19'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B19'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C19'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A20'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B20'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C20'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A21'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B21'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C21'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A22'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B22'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C22'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A23'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B23'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C23'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A24'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B24'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C24'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A25'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B25'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C25'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A26'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B26'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C26'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A27'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B27'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C27'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A28'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B28'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C28'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A29'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B29'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C29'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A30'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B30'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C30'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A31'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B31'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C31'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A32'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B32'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C32'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A33'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B33'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C33'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A34'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B34'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C34'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A35'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B35'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C35'
>>> ... so on.
>>>
>>> NOTE 5 [file topol.top, line 388]:
>>> System has non-zero total charge: 780.000004
>>> Total charge should normally be an integer. See
>>> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>>> for discussion on how close it should be to an integer.
>>>
>>>
>>>
>>> Analysing residue names:
>>> There are: 32280 Protein residues
>>> Analysing Protein...
>>> Number of degrees of freedom in T-Coupling group rest is 1529097.00
>>> This run will generate roughly 39 Mb of data
>>>
>>> There were 5 notes
>>>
>>> Back Off! I just backed up imd.tpr to ./#imd.tpr.1#
>>>
>>> gcq#97: "The Universe is Somewhere In Here" (J.G.E.M. Fraaije)
>>>
>>>
>>> I was only interested in non bonded terms (Specially GB-Energy), so I
>>> guess, exclusion of bonded terms is not a problem.
>>>
>> How are you excluding bonded terms? If you're hacking the topology to
>> remove the bonds, you're going to get a bunch of junk. I haven't followed
>> this entire thread fully, but if you're trying to just get certain energies
>> and not others, that's what mdrun -rerun is for. You don't initiate an
>> mdrun with a broken physical model, otherwise the output will be nonsense.
>>
>>
>> -Justin
>>
>>> Thanks,
>>> Jesmin
>>>
>>> On Wed, Aug 29, 2012 at 12:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>> On 8/29/12 11:27 AM, jesmin jahan wrote:
>>>>>
>>>>> Ops!
>>>>>
>>>>> Thanks Justin for you quick reply.
>>>>> Sorry, I have attached a log file from previous run. I am attaching
>>>>> the correct log file here. Please have a look.
>>>>>
>>>> I don't see a new .log file attached anywhere.
>>>>
>>>>
>>>>> Actually, I am a Computer Science student. I do not have enough
>>>>> background of Molecular Dynamics.
>>>>> I am using these three commands and
>>>>>
>>>>> pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none
>>>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr
>>>>> OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr
>>>>>
>>>>> and my .mdp file is like this:
>>>>>
>>>>> constraints = none
>>>>> integrator = md
>>>>> pbc = no
>>>>> dt = 0.001 ; ps
>>>>> nsteps = 0 ; 100000 ps = 100 ns
>>>>> rcoulomb = 1
>>>>> rvdw = 1
>>>>> rlist =1
>>>>> nstgbradii = 1
>>>>> rgbradii = 1
>>>>> implicit_solvent = GBSA
>>>>> gb_algorithm = HCT ; OBC ; Still
>>>>> sa_algorithm = None
>>>>>
>>>>>
>>>>> What else might go wrong?
>>>>>
>>>> The normal workflow included energy minimization before running MD.
>>>> Basic
>>>> tutorial material covers this. Without EM, you assume that whatever
>>>> structure you're using is suitable for MD, which may or may not be true.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>> Thanks,
>>>>> Jesmin
>>>>>
>>>>> On Wed, Aug 29, 2012 at 11:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 8/29/12 11:11 AM, jesmin jahan wrote:
>>>>>>>
>>>>>>>
>>>>>>> Thanks Mark for your reply.
>>>>>>>
>>>>>>> For the time being, I admit your claim that I am comparing apple with
>>>>>>> orange.
>>>>>>> So, to investigate more, I run the simulation without any modification
>>>>>>> in parameter fields and force field I am using. My test data is CMV
>>>>>>> virus shell.
>>>>>>> I am using the following commands.
>>>>>>>
>>>>>>> pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none
>>>>>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr
>>>>>>> OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr
>>>>>>>
>>>>>>>
>>>>>>> The log file looks like this:
>>>>>>> :-) G R O M A C S (-:
>>>>>>>
>>>>>>> GROningen MAchine for Chemical Simulation
>>>>>>>
>>>>>>> :-) VERSION 4.6-dev-20120820-87e5bcf (-:
>>>>>>>
>>>>>>> Written by Emile Apol, Rossen Apostolov, Herman J.C.
>>>>>>> Berendsen,
>>>>>>> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton
>>>>>>> Feenstra,
>>>>>>> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter
>>>>>>> Meulenhoff,
>>>>>>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland
>>>>>>> Schulz,
>>>>>>> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>>>>>>
>>>>>>> Berk Hess, David van der Spoel, and Erik Lindahl.
>>>>>>>
>>>>>>> Copyright (c) 1991-2000, University of Groningen, The
>>>>>>> Netherlands.
>>>>>>> Copyright (c) 2001-2010, The GROMACS development team
>>>>>>> at
>>>>>>> Uppsala University & The Royal Institute of Technology,
>>>>>>> Sweden.
>>>>>>> check out http://www.gromacs.org for more information.
>>>>>>>
>>>>>>> This program is free software; you can redistribute it
>>>>>>> and/or
>>>>>>> modify it under the terms of the GNU General Public
>>>>>>> License
>>>>>>> as published by the Free Software Foundation; either
>>>>>>> version
>>>>>>> 2
>>>>>>> of the License, or (at your option) any later version.
>>>>>>>
>>>>>>> :-) mdrun_mpi (-:
>>>>>>>
>>>>>>>
>>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>>> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
>>>>>>> GROMACS 4: Algorithms for highly efficient, load-balanced, and
>>>>>>> scalable
>>>>>>> molecular simulation
>>>>>>> J. Chem. Theory Comput. 4 (2008) pp. 435-447
>>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>>
>>>>>>>
>>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>>> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H.
>>>>>>> J.
>>>>>>> C.
>>>>>>> Berendsen
>>>>>>> GROMACS: Fast, Flexible and Free
>>>>>>> J. Comp. Chem. 26 (2005) pp. 1701-1719
>>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>>
>>>>>>>
>>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>>> E. Lindahl and B. Hess and D. van der Spoel
>>>>>>> GROMACS 3.0: A package for molecular simulation and trajectory
>>>>>>> analysis
>>>>>>> J. Mol. Mod. 7 (2001) pp. 306-317
>>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>>
>>>>>>>
>>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>>> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
>>>>>>> GROMACS: A message-passing parallel molecular dynamics implementation
>>>>>>> Comp. Phys. Comm. 91 (1995) pp. 43-56
>>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>>
>>>>>>> Input Parameters:
>>>>>>> integrator = md
>>>>>>> nsteps = 0
>>>>>>> init-step = 0
>>>>>>> ns-type = Grid
>>>>>>> nstlist = 10
>>>>>>> ndelta = 2
>>>>>>> nstcomm = 10
>>>>>>> comm-mode = Linear
>>>>>>> nstlog = 1000
>>>>>>> nstxout = 0
>>>>>>> nstvout = 0
>>>>>>> nstfout = 0
>>>>>>> nstcalcenergy = 10
>>>>>>> nstenergy = 100
>>>>>>> nstxtcout = 0
>>>>>>> init-t = 0
>>>>>>> delta-t = 0.001
>>>>>>> xtcprec = 1000
>>>>>>> nkx = 0
>>>>>>> nky = 0
>>>>>>> nkz = 0
>>>>>>> pme-order = 4
>>>>>>> ewald-rtol = 1e-05
>>>>>>> ewald-geometry = 0
>>>>>>> epsilon-surface = 0
>>>>>>> optimize-fft = FALSE
>>>>>>> ePBC = no
>>>>>>> bPeriodicMols = FALSE
>>>>>>> bContinuation = FALSE
>>>>>>> bShakeSOR = FALSE
>>>>>>> etc = No
>>>>>>> bPrintNHChains = FALSE
>>>>>>> nsttcouple = -1
>>>>>>> epc = No
>>>>>>> epctype = Isotropic
>>>>>>> nstpcouple = -1
>>>>>>> tau-p = 1
>>>>>>> ref-p (3x3):
>>>>>>> ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> compress (3x3):
>>>>>>> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> refcoord-scaling = No
>>>>>>> posres-com (3):
>>>>>>> posres-com[0]= 0.00000e+00
>>>>>>> posres-com[1]= 0.00000e+00
>>>>>>> posres-com[2]= 0.00000e+00
>>>>>>> posres-comB (3):
>>>>>>> posres-comB[0]= 0.00000e+00
>>>>>>> posres-comB[1]= 0.00000e+00
>>>>>>> posres-comB[2]= 0.00000e+00
>>>>>>> rlist = 1
>>>>>>> rlistlong = 1
>>>>>>> rtpi = 0.05
>>>>>>> coulombtype = Cut-off
>>>>>>> rcoulomb-switch = 0
>>>>>>> rcoulomb = 1
>>>>>>> vdwtype = Cut-off
>>>>>>> rvdw-switch = 0
>>>>>>> rvdw = 1
>>>>>>> epsilon-r = 1
>>>>>>> epsilon-rf = inf
>>>>>>> tabext = 1
>>>>>>> implicit-solvent = GBSA
>>>>>>> gb-algorithm = HCT
>>>>>>> gb-epsilon-solvent = 80
>>>>>>> nstgbradii = 1
>>>>>>> rgbradii = 1
>>>>>>> gb-saltconc = 0
>>>>>>> gb-obc-alpha = 1
>>>>>>> gb-obc-beta = 0.8
>>>>>>> gb-obc-gamma = 4.85
>>>>>>> gb-dielectric-offset = 0.009
>>>>>>> sa-algorithm = None
>>>>>>> sa-surface-tension = 2.25936
>>>>>>> DispCorr = No
>>>>>>> bSimTemp = FALSE
>>>>>>> free-energy = no
>>>>>>> nwall = 0
>>>>>>> wall-type = 9-3
>>>>>>> wall-atomtype[0] = -1
>>>>>>> wall-atomtype[1] = -1
>>>>>>> wall-density[0] = 0
>>>>>>> wall-density[1] = 0
>>>>>>> wall-ewald-zfac = 3
>>>>>>> pull = no
>>>>>>> rotation = FALSE
>>>>>>> disre = No
>>>>>>> disre-weighting = Conservative
>>>>>>> disre-mixed = FALSE
>>>>>>> dr-fc = 1000
>>>>>>> dr-tau = 0
>>>>>>> nstdisreout = 100
>>>>>>> orires-fc = 0
>>>>>>> orires-tau = 0
>>>>>>> nstorireout = 100
>>>>>>> dihre-fc = 0
>>>>>>> em-stepsize = 0.01
>>>>>>> em-tol = 10
>>>>>>> niter = 20
>>>>>>> fc-stepsize = 0
>>>>>>> nstcgsteep = 1000
>>>>>>> nbfgscorr = 10
>>>>>>> ConstAlg = Lincs
>>>>>>> shake-tol = 0.0001
>>>>>>> lincs-order = 4
>>>>>>> lincs-warnangle = 30
>>>>>>> lincs-iter = 1
>>>>>>> bd-fric = 0
>>>>>>> ld-seed = 1993
>>>>>>> cos-accel = 0
>>>>>>> deform (3x3):
>>>>>>> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>>> adress = FALSE
>>>>>>> userint1 = 0
>>>>>>> userint2 = 0
>>>>>>> userint3 = 0
>>>>>>> userint4 = 0
>>>>>>> userreal1 = 0
>>>>>>> userreal2 = 0
>>>>>>> userreal3 = 0
>>>>>>> userreal4 = 0
>>>>>>> grpopts:
>>>>>>> nrdf: 9534
>>>>>>> ref-t: 0
>>>>>>> tau-t: 0
>>>>>>> anneal: No
>>>>>>> ann-npoints: 0
>>>>>>> acc: 0 0 0
>>>>>>> nfreeze: N N N
>>>>>>> energygrp-flags[ 0]: 0
>>>>>>> efield-x:
>>>>>>> n = 0
>>>>>>> efield-xt:
>>>>>>> n = 0
>>>>>>> efield-y:
>>>>>>> n = 0
>>>>>>> efield-yt:
>>>>>>> n = 0
>>>>>>> efield-z:
>>>>>>> n = 0
>>>>>>> efield-zt:
>>>>>>> n = 0
>>>>>>> bQMMM = FALSE
>>>>>>> QMconstraints = 0
>>>>>>> QMMMscheme = 0
>>>>>>> scalefactor = 1
>>>>>>> qm-opts:
>>>>>>> ngQM = 0
>>>>>>>
>>>>>>> Initializing Domain Decomposition on 16 nodes
>>>>>>> Dynamic load balancing: auto
>>>>>>> Will sort the charge groups at every domain (re)decomposition
>>>>>>> Minimum cell size due to bonded interactions: 0.000 nm
>>>>>>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>>>>>>> Optimizing the DD grid for 16 cells with a minimum initial size of
>>>>>>> 0.000
>>>>>>> nm
>>>>>>> Domain decomposition grid 4 x 4 x 1, separate PME nodes 0
>>>>>>> Domain decomposition nodeid 0, coordinates 0 0 0
>>>>>>>
>>>>>>> Detecting CPU-specific acceleration. Present hardware specification:
>>>>>>> Vendor: GenuineIntel
>>>>>>> Brand: Intel(R) Xeon(R) CPU X5680 @ 3.33GHz
>>>>>>> Family: 6 Model: 44 Stepping: 2
>>>>>>> Features: htt sse2 sse4.1 aes rdtscp
>>>>>>> Acceleration most likely to fit this hardware: SSE4.1
>>>>>>> Acceleration selected at Gromacs compile time: SSE4.1
>>>>>>>
>>>>>>> Table routines are used for coulomb: FALSE
>>>>>>> Table routines are used for vdw: FALSE
>>>>>>> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
>>>>>>> System total charge: 6.000
>>>>>>> Configuring nonbonded kernels...
>>>>>>> Configuring standard C nonbonded kernels...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Linking all bonded interactions to atoms
>>>>>>>
>>>>>>> The initial number of communication pulses is: X 2 Y 2
>>>>>>> The initial domain decomposition cell size is: X 0.79 nm Y 0.89 nm
>>>>>>>
>>>>>>> The maximum allowed distance for charge groups involved in
>>>>>>> interactions
>>>>>>> is:
>>>>>>> non-bonded interactions 1.000 nm
>>>>>>> (the following are initial values, they could change due to box
>>>>>>> deformation)
>>>>>>> two-body bonded interactions (-rdd) 1.000 nm
>>>>>>> multi-body bonded interactions (-rdd) 0.794 nm
>>>>>>>
>>>>>>> When dynamic load balancing gets turned on, these settings will change
>>>>>>> to:
>>>>>>> The maximum number of communication pulses is: X 2 Y 2
>>>>>>> The minimum size for domain decomposition cells is 0.500 nm
>>>>>>> The requested allowed shrink of DD cells (option -dds) is: 0.80
>>>>>>> The allowed shrink of domain decomposition cells is: X 0.63 Y 0.56
>>>>>>> The maximum allowed distance for charge groups involved in
>>>>>>> interactions
>>>>>>> is:
>>>>>>> non-bonded interactions 1.000 nm
>>>>>>> two-body bonded interactions (-rdd) 1.000 nm
>>>>>>> multi-body bonded interactions (-rdd) 0.500 nm
>>>>>>>
>>>>>>>
>>>>>>> Making 2D domain decomposition grid 4 x 4 x 1, home cell index 0 0 0
>>>>>>>
>>>>>>> Center of mass motion removal mode is Linear
>>>>>>> We have the following groups for center of mass motion removal:
>>>>>>> 0: rest
>>>>>>> There are: 3179 Atoms
>>>>>>> Charge group distribution at step 0: 84 180 252 196 237 210 255 157
>>>>>>> 254 197 266 176 186 104 224 201
>>>>>>> Grid: 4 x 4 x 4 cells
>>>>>>> Initial temperature: 0 K
>>>>>>>
>>>>>>> Started mdrun on node 0 Wed Aug 29 02:32:21 2012
>>>>>>>
>>>>>>> Step Time Lambda
>>>>>>> 0 0.00000 0.00000
>>>>>>>
>>>>>>> Energies (kJ/mol)
>>>>>>> GB Polarization LJ (SR) Coulomb (SR) Potential
>>>>>>> Kinetic
>>>>>>> En.
>>>>>>> -1.65116e+04 5.74908e+08 -2.37699e+05 5.74654e+08
>>>>>>> 6.36009e+11
>>>>>>> Total Energy Temperature Pressure (bar)
>>>>>>> 6.36584e+11 1.60465e+10 0.00000e+00
>>>>>>>
>>>>>>> <====== ############### ==>
>>>>>>> <==== A V E R A G E S ====>
>>>>>>> <== ############### ======>
>>>>>>>
>>>>>>> Statistics over 1 steps using 1 frames
>>>>>>>
>>>>>>> Energies (kJ/mol)
>>>>>>> GB Polarization LJ (SR) Coulomb (SR) Potential
>>>>>>> Kinetic
>>>>>>> En.
>>>>>>> -1.65116e+04 5.74908e+08 -2.37699e+05 5.74654e+08
>>>>>>> 6.36009e+11
>>>>>>> Total Energy Temperature Pressure (bar)
>>>>>>> 6.36584e+11 1.60465e+10 0.00000e+00
>>>>>>>
>>>>>>> Total Virial (kJ/mol)
>>>>>>> -1.13687e+09 1.14300e+07 -1.23884e+07
>>>>>>> 1.14273e+07 -1.15125e+09 -5.31658e+06
>>>>>>> -1.23830e+07 -5.31326e+06 -1.16512e+09
>>>>>>>
>>>>>>> Pressure (bar)
>>>>>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>>>>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>>>>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>>>>>>
>>>>>>> Total Dipole (D)
>>>>>>> 1.35524e+03 -4.39059e+01 2.16985e+03
>>>>>>>
>>>>>>>
>>>>>>> M E G A - F L O P S A C C O U N T I N G
>>>>>>>
>>>>>>> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
>>>>>>> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
>>>>>>> NF=No Forces
>>>>>>>
>>>>>>> Computing: M-Number M-Flops
>>>>>>> %
>>>>>>> Flops
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------------------------
>>>>>>> Generalized Born Coulomb 0.006162 0.296
>>>>>>> 0.2
>>>>>>> GB Coulomb + LJ 0.446368 27.228
>>>>>>> 19.8
>>>>>>> Outer nonbonded loop 0.015554 0.156
>>>>>>> 0.1
>>>>>>> Born radii (HCT/OBC) 0.452530 82.813
>>>>>>> 60.3
>>>>>>> Born force chain rule 0.452530 6.788
>>>>>>> 4.9
>>>>>>> NS-Pairs 0.940291 19.746
>>>>>>> 14.4
>>>>>>> Reset In Box 0.003179 0.010
>>>>>>> 0.0
>>>>>>> CG-CoM 0.006358 0.019
>>>>>>> 0.0
>>>>>>> Virial 0.003899 0.070
>>>>>>> 0.1
>>>>>>> Stop-CM 0.006358 0.064
>>>>>>> 0.0
>>>>>>> Calc-Ekin 0.006358 0.172
>>>>>>> 0.1
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------------------------
>>>>>>> Total 137.361
>>>>>>> 100.0
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>>>>>>>
>>>>>>> av. #atoms communicated per step for force: 2 x 7369.0
>>>>>>>
>>>>>>>
>>>>>>> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>>>>>>>
>>>>>>> Computing: Nodes Number G-Cycles Seconds %
>>>>>>>
>>>>>>> -----------------------------------------------------------------------
>>>>>>> Domain decomp. 16 1 0.210 0.1
>>>>>>> 11.4
>>>>>>> Comm. coord. 16 1 0.006 0.0
>>>>>>> 0.3
>>>>>>> Neighbor search 16 1 0.118 0.1
>>>>>>> 6.4
>>>>>>> Force 16 1 1.319 0.8
>>>>>>> 71.4
>>>>>>> Wait + Comm. F 16 1 0.016 0.0
>>>>>>> 0.9
>>>>>>> Update 16 1 0.003 0.0
>>>>>>> 0.2
>>>>>>> Comm. energies 16 1 0.093 0.1
>>>>>>> 5.0
>>>>>>> Rest 16 0.082 0.1
>>>>>>> 4.4
>>>>>>>
>>>>>>> -----------------------------------------------------------------------
>>>>>>> Total 16 1.847 1.1
>>>>>>> 100.0
>>>>>>>
>>>>>>> -----------------------------------------------------------------------
>>>>>>>
>>>>>>> NOTE: 5 % of the run time was spent communicating energies,
>>>>>>> you might want to use the -gcom option of mdrun
>>>>>>>
>>>>>>>
>>>>>>> Parallel run - timing based on wallclock.
>>>>>>>
>>>>>>> NODE (s) Real (s) (%)
>>>>>>> Time: 0.036 0.036 100.0
>>>>>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>>>>>>> Performance: 12.702 3.856 2.425 9.896
>>>>>>> Finished mdrun on node 0 Wed Aug 29 02:32:21 2012
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The GB- energy value reported is half of that reported by Amber 11 and
>>>>>>> Octree based Molecular dynamic package.
>>>>>>>
>>>>>>> Although I guess the difference can be due to the difference in
>>>>>>> algorithms they are using, but there could be some other reason.
>>>>>>> If anyone knows what are the possible reasons behind this, please let
>>>>>>> me know. May be fixing them will give me same value for all different
>>>>>>> Molecular Dynamic Package.
>>>>>>>
>>>>>> I wouldn't trust the result you're getting here - the energy values and
>>>>>> temperature (10^10, yikes!) suggest there is something very wrong with
>>>>>> the
>>>>>> starting configuration.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Research Scientist
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>
>>>>>> ========================================
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>> ------
>>> jesmin
>>>
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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