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Hi GMX users,<br>
<br>
I am trying to continue a simulation that was run serially, now using
mdrun_mpi(parallel).<br>
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?<br>
I want to confirm whether the following grompp command is working for
the correct continuation of simulation or not.<br>
###############################################################################################<br>
grompp -f mdout.mdp -c mod.gro -t rerereafter15_WT.trr -o test.tpr -p
1cyp_WT.top -np 4 -time 20000<br>
:-) G R O M A C S (-:<br>
<br>
S C A M O R G<br>
<br>
:-) VERSION 3.1.4 (-:<br>
<br>
<br>
Copyright (c) 1991-2002, University of Groningen, The Netherlands<br>
This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br>
as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br>
<br>
:-)
/users/sridhar/bin/GROMACS3_1_4/x86_64-unknown-linux-gnu/bin/grompp (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-f mdout.mdp Input, Opt! grompp input file with MD parameters<br>
-po mdout.mdp Output grompp input file with MD parameters<br>
-c mod.gro Input Generic structure: gro g96 pdb tpr
tpb tpa<br>
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr
tpb tpa<br>
-n index.ndx Input, Opt. Index file<br>
-deshuf deshuf.ndx Output, Opt. Index file<br>
-p 1cyp_WT.top Input Topology file<br>
-pp processed.top Output, Opt. Topology file<br>
-o test.tpr Output Generic run input: tpr tpb tpa<br>
-t rerereafter15_WT.trr Input, Opt! Full precision trajectory: trr
trj<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-[no]X bool no Use dialog box GUI to edit command line
options<br>
-nice int 0 Set the nicelevel<br>
-[no]v bool yes Be loud and noisy<br>
-time real 20000 Take frame at or first after this time.<br>
-np int 4 Generate statusfile for # nodes<br>
-[no]shuffle bool no Shuffle molecules over nodes<br>
-[no]sort bool no Sort molecules according to X coordinate<br>
-[no]rmdumbds bool yes Remove constant bonded interactions with
dummies<br>
-load string Releative load capacity of each node on a
parallel<br>
machine. Be sure to use quotes around the
string,<br>
which should contain a number for each node<br>
-maxwarn int 10 Number of warnings after which input
processing<br>
stops<br>
-[no]check14 bool no Remove 1-4 interactions without Van der
Waals<br>
<br>
creating statusfile for 4 nodes...<br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#<br>
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar<br>
checking input for internal consistency...<br>
calling /usr/bin/cpp...<br>
processing topology...<br>
Generated 135 of the 1081 non-bonded parameter combinations<br>
WARNING 1 [file "1cyp_WT_A.itp", line 9279]:<br>
No default G96Bond types, using zeroes<br>
WARNING 2 [file "1cyp_WT_A.itp", line 24306]:<br>
No default G96Angle types, using zeroes<br>
WARNING 3 [file "1cyp_WT_A.itp", line 25181]:<br>
No default G96Angle types, using zeroes<br>
WARNING 4 [file "1cyp_WT_A.itp", line 25182]:<br>
No default G96Angle types, using zeroes<br>
WARNING 5 [file "1cyp_WT_A.itp", line 25183]:<br>
No default G96Angle types, using zeroes<br>
WARNING 6 [file "1cyp_WT_A.itp", line 25184]:<br>
No default G96Angle types, using zeroes<br>
WARNING 7 [file "1cyp_WT_A.itp", line 27551]:<br>
No default Proper Dih. types, using zeroes<br>
Excluding 3 bonded neighbours for Protein_A 1<br>
turning all bonds into constraints...<br>
Excluding 3 bonded neighbours for Protein_B 1<br>
turning all bonds into constraints...<br>
Excluding 1 bonded neighbours for SOL 12304<br>
turning all bonds into constraints...<br>
processing coordinates...<br>
double-checking input for internal consistency...<br>
Velocities were taken from a Maxwell distribution at 300 K<br>
renumbering atomtypes...<br>
converting bonded parameters...<br>
# G96ANGLES: 29340<br>
# PDIHS: 13075<br>
# IDIHS: 12905<br>
# LJ14: 23997<br>
# CONSTR: 15033<br>
# SETTLE: 24608<br>
Walking down the molecule graph to make shake-blocks<br>
initialising group options...<br>
processing index file...<br>
Analysing residue names:<br>
Opening library file
/users/sridhar/bin/GROMACS3_1_4/share/gromacs/top/aminoacids.dat<br>
There are: 12308 OTHER residues<br>
There are: 478 PROTEIN residues<br>
There are: 0 DNA residues<br>
Analysing Protein...<br>
Analysing Other...<br>
Making dummy/rest group for Acceleration containing 41820 elements<br>
Making dummy/rest group for Freeze containing 41820 elements<br>
Making dummy/rest group for VCM containing 41820 elements<br>
Number of degrees of freedom in T-Coupling group Protein is 9617.15<br>
Number of degrees of freedom in T-Coupling group HEME is 86.50<br>
Number of degrees of freedom in T-Coupling group SOL is 73821.35<br>
Number of degrees of freedom in T-Coupling group CL- is 9.00<br>
Making dummy/rest group for User1 containing 41820 elements<br>
Making dummy/rest group for User2 containing 41820 elements<br>
Making dummy/rest group for XTC containing 41820 elements<br>
Making dummy/rest group for Or. Res. Fit containing 41820 elements<br>
T-Coupling has 4 element(s): Protein HEME SOL CL-<br>
Energy Mon. has 4 element(s): Protein HEME SOL CL-<br>
Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>
User1 has 1 element(s): rest<br>
User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>
XTC has 1 element(s): rest<br>
Or. Res. Fit has 1 element(s): rest<br>
Checking consistency between energy and charge groups...<br>
getting data from old trajectory ...<br>
Reading Coordinates and Box size from old trajectory<br>
Will read till time 20000<br>
<font color="#ff0000">Velocities generated: ignoring velocities in
input trajectory</font><br>
trn version: GMX_trn_file<br>
Reading frame 680 time 19997.312 Using frame at t = 20000 ps<br>
Starting time for run is 0 ps<br>
Calculating fourier grid dimensions for X Y Z<br>
Using a fourier grid of 72x56x75, spacing 0.111 0.114 0.117<br>
splitting topology...<br>
Walking down the molecule graph to make shake-blocks<br>
There are 14390 charge group borders and 12308 shake borders<br>
There are 12308 total borders<br>
Division over nodes in atoms:<br>
10455 10455 10455 10455<br>
writing run input file...<br>
<br>
Back Off! I just backed up test.tpr to ./#test.tpr.4#<br>
There were 7 warnings<br>
<br>
gcq#142: "It Was My Pleasure" (Pulp Fiction)<br>
#############################################################################<br>
<pre class="moz-signature" cols="72">--
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
<a class="moz-txt-link-freetext" href="http://www.cdfd.org.in">http://www.cdfd.org.in</a>
email: <a class="moz-txt-link-abbreviated" href="mailto:sridhar@cdfd.org.in">sridhar@cdfd.org.in</a>
Phone: Lab: 08413-235467*2044
Mobile: 9866147193
</pre>
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