[gmx-users] Problem with incorrect GB-Polarization Energy Value
jesmin jahan
shraban03 at gmail.com
Wed Aug 29 19:06:09 CEST 2012
Dear Justin,
Thanks for your reply.
Here is the CMV.log file . Please check it.
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.
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.
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
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.
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
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>>
>>
>>
>>
>>
>>
>
> --
> ========================================
>
> 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
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