[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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