[gmx-users] Re: Protein coming out of the box

[Tsjerk Wassenaar]

Ravi,

Just come to terms with PBC: the box has no outside. Chapter 3 of the manual...

Tsjerk

On Sat, Oct 11, 2008 at 1:30 PM, ravi sharma <rdsharma_4u at yahoo.com> wrote:
> So how could i do this energy conservation,
>
>
> Ravi Datta Sharma
> Lecturer,
> Bioinformatics,
> Department of Microbiology,
> CCS Unversity,
> Meerut
>
>
>
> --- On Sat, 11/10/08, sudheer babu <sudheer.pbm07 at gmail.com> wrote:
>
> From: sudheer babu <sudheer.pbm07 at gmail.com>
> Subject: [gmx-users] Re: Protein coming out of the box
> To: gmx-users at gromacs.org
> Date: Saturday, 11 October, 2008, 4:46 PM
>
> Oh...Similar type of problem once I have got, so got reply from some one in
> archives that if use comm_grps= protein , protein will not come out of the
> water box.So
>  thats why I have suggested, If I say wrong answer regret for that
>
>
>>  Hi,
>>  Ravi
>>  Use comm_grps = protein in your .mdp file.
>>
>>
>>       3. protein coming out of the box (ravi sharma)
>>
>
>
> No!
>
> You will ruin energy conservation...
>
>>
>>     Hello everyone
>>
>>     my protein coming out of the box in final md how can i fix my
>>     protein in the middle of the box. can you help me out??
>
>>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623