[gmx-users] High rmsf value

Justin Lemkul jalemkul at vt.edu
Sat Apr 21 18:30:37 CEST 2018

On 4/21/18 12:24 PM, SAYAN BHATTACHARJEE wrote:
> 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.


If you have a complex, don't try to center on the entire thing. Choose 
one chain of the complex and center on that. If elements of the complex 
are split on opposing "faces" of the box, their center is still 
(geometrically speaking) coincident with the actual center of the box, 
so trjconv works properly but it's not what you want.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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