[gmx-users] Continuation of Serial MD simulation in Parallel

Sridhar Acharya sridharfirst at gmail.com
Mon Jul 3 09:31:16 CEST 2006


Hi GMX users,

I am trying to continue a simulation that was run serially, now using 
mdrun_mpi(parallel).
So I am generating .tpr file as follows using the command as follows. 
Does the log message (Highlighted in RED) "Velocities generated: 
ignoring velocities in input trajectory", means that the simulation wont 
be continuation of the earlier one?
I want to confirm whether the following grompp command is working for 
the correct continuation of simulation or not.
###############################################################################################
grompp -f mdout.mdp -c mod.gro -t rerereafter15_WT.trr -o test.tpr -p 
1cyp_WT.top -np 4 -time 20000
                         :-)  G  R  O  M  A  C  S  (-:

                              S  C  A  M  O  R  G

                            :-)  VERSION 3.1.4  (-:


       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         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.

 :-)  
/users/sridhar/bin/GROMACS3_1_4/x86_64-unknown-linux-gnu/bin/grompp  (-:

Option     Filename  Type          Description
------------------------------------------------------------
  -f      mdout.mdp  Input, Opt!   grompp input file with MD parameters
 -po      mdout.mdp  Output        grompp input file with MD parameters
  -c        mod.gro  Input         Generic structure: gro g96 pdb tpr 
tpb tpa
  -r       conf.gro  Input, Opt.   Generic structure: gro g96 pdb tpr 
tpb tpa
  -n      index.ndx  Input, Opt.   Index file
-deshuf  deshuf.ndx  Output, Opt.  Index file
  -p    1cyp_WT.top  Input         Topology file
 -pp  processed.top  Output, Opt.  Topology file
  -o       test.tpr  Output        Generic run input: tpr tpb tpa
  -t rerereafter15_WT.trr  Input, Opt!   Full precision trajectory: trr trj

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int      0  Set the nicelevel
      -[no]v   bool    yes  Be loud and noisy
       -time   real  20000  Take frame at or first after this time.
         -np    int      4  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X coordinate
-[no]rmdumbds  bool    yes  Remove constant bonded interactions with dummies
       -load string         Releative load capacity of each node on a 
parallel
                            machine. Be sure to use quotes around the 
string,
                            which should contain a number for each node
    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals

creating statusfile for 4 nodes...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 135 of the 1081 non-bonded parameter combinations
WARNING 1 [file "1cyp_WT_A.itp", line 9279]:
  No default G96Bond types, using zeroes
WARNING 2 [file "1cyp_WT_A.itp", line 24306]:
  No default G96Angle types, using zeroes
WARNING 3 [file "1cyp_WT_A.itp", line 25181]:
  No default G96Angle types, using zeroes
WARNING 4 [file "1cyp_WT_A.itp", line 25182]:
  No default G96Angle types, using zeroes
WARNING 5 [file "1cyp_WT_A.itp", line 25183]:
  No default G96Angle types, using zeroes
WARNING 6 [file "1cyp_WT_A.itp", line 25184]:
  No default G96Angle types, using zeroes
WARNING 7 [file "1cyp_WT_A.itp", line 27551]:
  No default Proper Dih. types, using zeroes
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for Protein_B 1
turning all bonds into constraints...
Excluding 1 bonded neighbours for SOL 12304
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
#  G96ANGLES:   29340
#      PDIHS:   13075
#      IDIHS:   12905
#       LJ14:   23997
#     CONSTR:   15033
#     SETTLE:   24608
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file 
/users/sridhar/bin/GROMACS3_1_4/share/gromacs/top/aminoacids.dat
There are: 12308      OTHER residues
There are:   478    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for Acceleration containing 41820 elements
Making dummy/rest group for Freeze containing 41820 elements
Making dummy/rest group for VCM containing 41820 elements
Number of degrees of freedom in T-Coupling group Protein is 9617.15
Number of degrees of freedom in T-Coupling group HEME is 86.50
Number of degrees of freedom in T-Coupling group SOL is 73821.35
Number of degrees of freedom in T-Coupling group CL- is 9.00
Making dummy/rest group for User1 containing 41820 elements
Making dummy/rest group for User2 containing 41820 elements
Making dummy/rest group for XTC containing 41820 elements
Making dummy/rest group for Or. Res. Fit containing 41820 elements
T-Coupling       has 4 element(s): Protein HEME SOL CL-
Energy Mon.      has 4 element(s): Protein HEME SOL CL-
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
Checking consistency between energy and charge groups...
getting data from old trajectory ...
Reading Coordinates and Box size from old trajectory
Will read till time 20000
Velocities generated: ignoring velocities in input trajectory
trn version: GMX_trn_file
Reading frame     680 time 19997.312   Using frame at t = 20000 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x56x75, spacing 0.111 0.114 0.117
splitting topology...
Walking down the molecule graph to make shake-blocks
There are 14390 charge group borders and 12308 shake borders
There are 12308 total borders
Division over nodes in atoms:
 10455 10455 10455 10455
writing run input file...

Back Off! I just backed up test.tpr to ./#test.tpr.4#
There were 7 warnings

gcq#142: "It Was My Pleasure" (Pulp Fiction)
#############################################################################

-- 
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: sridhar at cdfd.org.in
Phone: Lab: 08413-235467*2044
Mobile: 9866147193


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