[gmx-users] pbc

[kannan]

Thank you for your reply Tsjerk..
I do many Trjconv -pbc mol -ur compact -center. but it doesn't help..

this is PBC. if i center protein the ligand goes other side at end of
simulation. if i center ligand, then protein goes... if i center both, its
trajectory is same as old one.

How to overcome this problem? Please give some suggestion.

or shall i analyse without trjconv -pbc with raw trajector?

Thank you
best regards,
kannan s


On Fri, Jan 31, 2014 at 5:03 PM, Tsjerk Wassenaar [via GROMACS] <
ml-node+s5086n5014189h6 at n6.nabble.com> wrote:

> Hi Kannan,
>
> Depends a bit. Some tools handle PBC properly, some don't.
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, Jan 31, 2014 at 9:30 AM, Kannan S <[hidden email]<http://user/SendEmail.jtp?type=node&node=5014189&i=0>>
> wrote:
>
> > Is there any problem when we analyse the protein-ligand complex
> simulation
> > withPBC problem without using -trjconv?
> >
> > Thank you
> > kannan s
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> Tsjerk A. Wassenaar, Ph.D.
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