<br clear="all"><br>Dear All,<br> 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 <a href="http://simulation.it">simulation.it</a> was crashed before, so I used tpbconv -f previous.trr -e previous.edr -s previous.tpr -o new.tpr -until 20000<br>
then gave the command --><br> mdrun -s new.tpr -o new.trr -c new.gro -g new.log -e new.edr<br><br>now job is running....<br><br>now for analysis I am giving this command<br>g_rms new.tpr -f new.trr -o new_rmsd.xvg -xvgr<br>
<br>it is giving this output<br>:-) g_rms (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb xml<br>
-f new.trr Input Generic trajectory: xtc trr t pdb<br> -f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb<br> -n index.ndx Input, Opt. Index file<br> -o new_rmsd.xvg Output xvgr/xmgr file<br>
-mir rmsdmir.xvg Output, Opt. xvgr/xmgr file<br> -a avgrp.xvg Output, Opt. xvgr/xmgr file<br>-dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file<br> -m rmsd.xpm Output, Opt. X PixMap compatible matrix file<br>
-bin rmsd.dat Output, Opt. Generic data file<br> -bm bond.xpm Output, Opt. X PixMap compatible matrix file<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 19 Set the nicelevel<br> -b time 0 First frame (ps) to read from trajectory<br>
-e time 0 Last frame (ps) to read from trajectory<br> -dt time 0 Only use frame when t MOD dt = first time (ps)<br> -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h<br>
-[no]w bool no View output xvg, xpm, eps and pdb files<br> -[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace program<br> -what enum rmsd Structural difference measure: rmsd, rho or rhosc<br>
-[no]pbc bool yes PBC check<br> -fit enum rot+trans Fit to reference structure: rot+trans,<br> translation or none<br> -prev int 0 Compare with previous frame<br>
-[no]split bool no Split graph where time is zero<br> -skip int 1 Only write every nr-th frame to matrix<br> -skip2 int 1 Only write every nr-th frame to matrix<br> -max real -1 Maximum level in comparison matrix<br>
-min real -1 Minimum level in comparison matrix<br> -bmax real -1 Maximum level in bond angle matrix<br> -bmin real -1 Minimum level in bond angle matrix<br> -nlevels int 80 Number of levels in the matrices<br>
-ng int 1 Number of groups to compute RMS between<br><br>-------------------------------------------------------<br>Program g_rms, VERSION 3.3<br>Source code file: statutil.c, line: 787<br><br>Invalid command line argument:<br>
new.tpr<br>-------------------------------------------------------<br><br> WHY THIS IS SHOWING THIS ERROR?<br><br><br>Thanks in advance<br><br> Anamika<br><br>