Dear Amber Users,
As I said earlier I am using nscm=10 , now I need to calculate MSD of
selected residues in my system.I have simulations performed in periodic
boundary conditions at temperature above 300K.
For MSD calculations I remove the solvent and calculate the diffusion of
residues using ptraj .Is this right way of doing it or do I need to center
the trajectory and then calculate.I understood use of nscm , automatically
centers the trajectory after the required number of steps .
Thanks
John.
On Wed, Oct 27, 2010 at 2:17 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it depends on what rdf you want. usually you want to not only center the
> solute, but also do a best-fit. how you treat imaging is also important
> here. let us know more about your simulation conditions and what you want
> to
> calculate and we can help out.
>
> On Wed, Oct 27, 2010 at 1:15 PM, John S <s.john634.gmail.com> wrote:
>
> > Dear Amber Users
> > If I am using nscm =10 in my md protocol , the trajectory so obtained is
> > already a centered trajectory .
> > Do I need to center it again using ptraj before calculations for radial
> > distribution function.
> >
> > Thanks
> > John
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Received on Mon Nov 22 2010 - 22:30:03 PST
