[gmx-users] Problem with incorrect GB-Polarization Energy Value
jesmin jahan
shraban03 at gmail.com
Wed Aug 29 17:11:11 CEST 2012
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.
Best Regard,
Jesmin
On Mon, Aug 27, 2012 at 6:25 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 28/08/2012 2:33 AM, jesmin jahan wrote:
>>
>> Dear All,
>>
>> I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I
>> am not interested to any other energy terms right now, I have set all
>> the non-bonded parameters to 0.
>>
>> I am also calculating GB polarization energy using other available
>> Molecular Dynamic Packages and doing a comparative study between them
>> (say: Accuracy Vs. Speed Up).
>> I have already used Gromacs for calculating GB-energy for 168
>> different Protein molecules and the energy values reported were more
>> or less the same as reported by others.
>>
>> Now, I am using a virus shell as input in this process. It contains
>> 1.5 million atoms. Unfortunately, this time, the energy reported is
>> almost half of the value reported by others.
>> So, I am a little bit confused. Am I doing something wrong? I have
>> heard previously that there is no max size for Gromacs.
>
>
> Probably you're comparing apples with oranges. Your previous reports were
> choosing to use a cut-off in the non-bonded interactions. Perhaps some of
> the other codes are not or cannot. That would greatly affect performance and
> the value of the result, and is part of why it is meaningless to try to
> extract the time for just a part of a calculation without the timing of its
> support infrastructure (such as constructing the pair list from the
> cut-off). Also, since you are computing on proteins, you probably have
> bonded and VDW interactions in your force field also, and your timing
> comparisons will be misleading if you ignore those. The time taken to
> execute an implementation of a complex algorithm is rarely additive in its
> parts. For example, software that makes good or bad use of the cache in a
> real calculation won't have the opportunity to show that if the whole
> problem size fits in the L1 cache because it's been stripped down.
>
> Mark
> --
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--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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