I would also suggest to use the xtc and not the trr file for analysis.
The (compressed) xtc is usually written more often than the
(full-precision) trr.
Jochen
Anamika Awasthi wrote:
Dear All,
My protein is simulating for 20 ns and 16 ns has already over,
but I want to analyze RMSD and RMSF for this 16 ns simulation, without
stopping the running simulation.it <http://simulation.it> was crashed
before, so I used tpbconv -f previous.trr -e previous.edr -s
previous.tpr -o new.tpr -until 20000
then gave the command -->
mdrun -s new.tpr -o new.trr -c new.gro -g new.log -e new.edr
now job is running....
now for analysis I am giving this command
g_rms new.tpr -f new.trr -o new_rmsd.xvg -xvgr
it is giving this output
:-) g_rms (-:
Option Filename Type Description
------------------------------------------------------------
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro
g96 pdb xml
-f new.trr Input Generic trajectory: xtc trr t pdb
-f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro
g96 pdb
-n index.ndx Input, Opt. Index file
-o new_rmsd.xvg Output xvgr/xmgr file
-mir rmsdmir.xvg Output, Opt. xvgr/xmgr file
-a avgrp.xvg Output, Opt. xvgr/xmgr file
-dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file
-m rmsd.xpm Output, Opt. X PixMap compatible matrix file
-bin rmsd.dat Output, Opt. Generic data file
-bm bond.xpm Output, Opt. X PixMap compatible matrix file
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 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the
output
xvg files for the xmgrace program
-what enum rmsd Structural difference measure: rmsd, rho
or rhosc
-[no]pbc bool yes PBC check
-fit enum rot+trans Fit to reference structure: rot+trans,
translation or none
-prev int 0 Compare with previous frame
-[no]split bool no Split graph where time is zero
-skip int 1 Only write every nr-th frame to matrix
-skip2 int 1 Only write every nr-th frame to matrix
-max real -1 Maximum level in comparison matrix
-min real -1 Minimum level in comparison matrix
-bmax real -1 Maximum level in bond angle matrix
-bmin real -1 Minimum level in bond angle matrix
-nlevels int 80 Number of levels in the matrices
-ng int 1 Number of groups to compute RMS between
-------------------------------------------------------
Program g_rms, VERSION 3.3
Source code file: statutil.c, line: 787
Invalid command line argument:
new.tpr
-------------------------------------------------------
WHY THIS IS SHOWING THIS ERROR?
Thanks in advance
Anamika
------------------------------------------------------------------------
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--
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************
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