I am following Justin A. Lemkul, Ph.D. (Virginia Tech Department of Biochemistry) tutorails to run gromacs. Is there a command to get md_0_1.trr file after the completion of the simulation. I have enetered zero values to nstxout, nstfout, or nstvout in md.mdp file during the md run. Now I need to do a cluster analysis and without .trr file I cannot proceed.
Clustering requires coordinates, which you should have in an .xtc file. There is no requirement for a .trr file for this purpose.
Justin Lemkul :
Thank you very much for the reply. Here with I mentioned the codes that I am following and according to that, requires a .trr file. Could you please guide me through this?
g_rms –s ../md.tpr –f ../md.trr –f2 ../md.trr –m rmsd-matrix.xpm
g_cluster –s ../md.tpr –f ../md.trr –dm rmsd-matrix.xpm –dist rms- distribution.xvg –o clusters.xpm –sz cluster-sizes.xvg –tr cluster-transitions.xpm –ntr cluster-transitions.xvg –clid cluster-id-overtime.xvg –cl clusters.pdb –cutoff 0.25 –method gromos
Thank you.
Again, neither of those commands requires a .trr file. An .xtc file will work just fine. There is no use for full-precision coordinates for such simple operations.
Yasuri Amarasekara Use "md_0_1.xtc" instead of "md.trr" \
eg. g_rms –s ../md.tpr –f ../md.xtc –m rmsd-matrix.xpm instead of
g_rms –s ../md.tpr –f ../md.trr –f2 ../md.trr –m rmsd-matrix.xpm
Dr Thirumal Kumar D and Justin Lemkul : Thank you very much for the great help. It worked well.
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