Thanks Justin.
Are these two commands for RMSD OK after making index groups for protein only?
Forgive my silliness:
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc
mol -ur compact
Select 0
gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns
Select 4 4 for backbone atoms. I think then GROMACS will recognize only the
index groups will be used for identifying backbones
On Wednesday, 9 January, 2019, 8:30:52 PM IST, Justin Lemkul
<jalem...@vt.edu> wrote:
On 1/9/19 6:07 AM, Dr. Seema Mishra wrote:
> Hello
> Any idea how to generate RMSD plots for only the protein in a protein-peptide
> complex? I mean, do give me commands for using only the protein backbone
> atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not
> want peptide RMSD plots included.
Make an index group that includes only the atoms you want to analyze.
-Justin
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Justin A. Lemkul, Ph.D.
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