[gmx-users] Re: trjconv with multiple chains

yuanyuan wang yilin3201 at 126.com
Mon Jan 10 09:43:14 CET 2011

sorry to say I can not found a center for the trj.  I tried to make bigger box by trjconv -box -boxcenter, but it seems that the trj only exist in the old box area ,bigger box cannot stop jumps.
Is it really happened that I can do nothing with it ?
                                             yuanyuan wang
Message: 1
Date: Fri, 7 Jan 2011 02:56:08 -0800
From: Amit Choubey <kgp.amit at gmail.com>
Subject: Re: [gmx-users] trjconv with multiple chains
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Content-Type: text/plain; charset="iso-8859-1"

Make your box bigger?

2011/1/6 yuanyuan wang <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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