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 <jalem...@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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