[gmx-users] pbc

[kannan]

Thank you very much for your valuable suggestion Justin...

best regards,
kannan s

I


On Fri, Jan 31, 2014 at 6:31 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5014192h99 at n6.nabble.com> wrote:

>
>
> On 1/31/14, 7:09 AM, kannan wrote:
>
> > 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?
> >
>
> As Tsjerk said, some tools handle PBC well, some don't.  If you're having
> a
> specific issue with a specific tool, then you will need to account for
> periodicity effects.  If not, then there is no need to worry.  With
> protein-ligand systems and other complexes, -pbc nojump is usually the
> best
> first step.  See
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
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