[gmx-users] Trajectory optimization - 2 chains are separated

[Marwa Abd El Kader]

Dear Justin,
Would you please tell me how, give me an example code, because I'm a novice?

Thanks in advance,
Marwa

On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote:
> > Dear gmx-users mailing list team,
> > I want to know how to fix the separation of 2 chains after the production
> > run. I'm trying different combinations of trjconv after creating an index
> > file having a specific residue(s) on the interface between the 2 chains,
> > but nothing is working. I fixed this issue before but when there was only
> > one chain, now with 2 chains, I don't know how to rejoin them together
> > again. Can you suggest me any solution, please?!
> > *N.B: the 2 chains are considered as one when selected in VMD
>
> Center on a single chain rather than trying to work with the interface
> residues.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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