On 01/10/11, yuanyuan wang <[email protected]> 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 <[email protected]> > Subject: Re: [gmx-users] trjconv with multiple chains > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Make your box bigger? > > 2011/1/6 yuanyuan wang <[email protected]> > > > 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 > > > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > >
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