From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Fri Feb 16 2007 - 14:03:40 CST
>
> Dear Users,
> >
> > I am doing a constant velocity SMD. In this i am pulling a ligand out of
> > the protein (in waterbox) with the aim of seeing the conformational changes
> > in binding site both during the pulling and after the pulling of ligand. Now
> > with my given specifications, the ligand do gets pulled out from the protein
> > and keeps going in the defined vector direction but since the simulation is
> > long it crosses the box and enter it from the other side (due to PBC). So
> > now my question is, is there anyway in which i can put a command to stop
> > this pulling of ligand after a certain specified time in simulation or a
> > certain distance from the protein? Or do i have to just stop the simulation
> > and block the SMD commands (once the ligand gets pulled at certain distance)
> > and start the simulation again.
> >
>
Any suggestions would be of great help
> >
> > Thank you
> > singh
> >
> >
> >
> >
>
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