[gmx-users] regarding rmsd !!

[Jochen Hub]

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
************************************************