[gmx-users] How to change the default value for pbc ?

[Liu Shiyong]

Thanks.

It's exactly what you said.


      ePBC                 = no


On Thu, Mar 13, 2008 at 6:44 PM, Alan Dodd <anoddlad at yahoo.com> wrote:

> Editing mdout.mdp will not affect the parameters in your .tpr, and
> therefore your simulation, I'm fairly sure.  It's just a report of what
> you've specified, with all the defaults.
> Add the pbc=whatever line into your INPUT mdp to fix this.
>
> ----- Original Message ----
> From: Liu Shiyong <liushiyong at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, March 13, 2008 11:39:46 PM
> Subject: [gmx-users] How to change the default value for pbc ?
>
> Hi,
>
> I generated  mdout.mdp
>
> by   grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o
> ${file}.input.tpr .
>
> The pbc in mdout.mdp is like:
>
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc                      = xyz
>
> It seems that grompp doesnot give an option to change the pbc value.
>
> I didnot find an easy way to change the pbc value . The only way I found
> is to  edit the mdout.mdp directly.
>
> Best
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu>
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
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-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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