[gmx-users] Problem with incorrect GB-Polarization Energy Value
jesmin jahan
shraban03 at gmail.com
Wed Aug 29 17:27:27 CEST 2012
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.
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?
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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--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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