[gmx-users] Problem with incorrect GB-Polarization Energy Value
Justin Lemkul
jalemkul at vt.edu
Wed Aug 29 18:09:06 CEST 2012
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
>>
>> ========================================
>>
>> --
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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
========================================
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