[gmx-users] Re: trjconv with multiple chains

[Mark Abraham]

On 01/10/11, yuanyuan wang  <yilin3201 at 126.com> wrote:
> 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 ? 
> 
> 

No. Justin gave you a good suggestion. What happened when you tried it?

Mark


> 
> 
>                                              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>
> Message-ID:
> 	<AANLkTi=2=NfWA_budToyKiXZT5rdXRGNk7RHzXvN7bc=@mail.gmail.com>
> 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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