[gmx-users] trjconv with multiple chains
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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