[gmx-users] High rmsf value

[SAYAN BHATTACHARJEE]

Dear Lemkul,

My complex have two protein( Chain A & B) as dimer bound to DNA. So, I have
to make index consisting only chain A or B, excluding DNA, then center and
output options will both be chain A or B in  trjconv command?
Is it possible to select both chains A & B?

On Sat, 21 Apr 2018, 22:00 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> 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.
>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
>
> 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
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
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