[gmx-users] High rmsf value

[SAYAN BHATTACHARJEE]

I bave simulated protein_dna complex for 500ns following gromacs manuals,
during visualisation in vmd its doesn't maintain pbc, moves out from box. I
have tried those following commands, but failed to make my complex within
box throughout trajectory marging protein and dna only in index.

I have tried,

1. Trjconv -f 500ns.xtc -s md_0_1.tpr -pbc cluster -n protein_dna.ndx -o
center.xtc -ur compact  -center

Auto select protein_dna from input index for both centering and output.

I have tried -pbc mol option too but it didn't work here.
Visualisation in vmd is now fine(using cluster option and loading
center.xtc trajectory), complex is now within box, but, in the next step
when I tried nojump option and fit with reference initial structure by
uising the following commands, pbc condition didn't maintain and protein
motion was horrible and the rmsf shows very high value(using  fit.xtc/
nojump.xtc/ centre.xtc for rmsf calculation).

2.Trjconv -f center.xtc -s md_0_1.tpr -pbc nojump -n protein_dna.ndx -o
nojump.xtc

3.Trjconv -f  nojump.xtc -s md_0_1.tpr -fit rot+trans -n protein_dna.ndx -o
fit.xtc

Please give suggestions in this regard.