[gmx-users] Problem with incorrect GB-Polarization Energy Value
Justin Lemkul
jalemkul at vt.edu
Wed Aug 29 19:11:13 CEST 2012
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
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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
>
>
>
--
========================================
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
========================================
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