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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: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 |
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