[gmx-users] trjconv with multiple chains

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 7 13:07:39 CET 2011

Amit Choubey wrote:
> Make your box bigger?

Box size is unrelated to trjconv.  Periodicity effects will still apply - things 
will diffuse no matter how large you try to make the box.


> 2011/1/6 yuanyuan wang <yilin3201 at 126.com <mailto:yilin3201 at 126.com>>
>     dear all,
>              I am doing a simulation that have many chains in a box ,
>     and I can find a center for them after serval tries.
>              I use almost every option of trjconv,-pbc
>     mol,atom,res,whole,nojump , -ur compact, -center , -box to got
>     bigger box, and -boxcenter, -fit ..
>              still some chain cannot convert into box. them jump from
>     one box to another ,
>              is there any ways that they not jump to another box?
>              thanks a lot.
>     yuanyuan
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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