[gmx-users] trjconv with multiple chains

ms devicerandom at gmail.com
Fri Jan 7 17:05:39 CET 2011

On 07/01/11 02:17, yuanyuan wang wrote:
> 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.

If they do cluster together fast (like mine), the solution I found -with 
the help of Justin Lemkul, if I remember correctly- was to use trjconv 
for simply centering on one of the chains. This way the aggregate, once 
formed, stayed in the center.

If they just diffuse, I suspect there's nothing you can do: you have 
stuff diffusing in a periodic system, and WYSIWYG.


Massimo Sandal, Ph.D.

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