[gmx-users] regarding rmsd !!

[Anamika Awasthi]

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 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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