if by MSD you mean root mean square deviations (rmsd) then you can use the
rms command in ptraj. if you don't want the root, you can square the values
afterward. you do not need to center the trajectory first, since rms does a
best-fit prior to the calculation of deviation.
note however, that this doesn't give you the "diffusion of residues" that
you mentioned. you'll need to be more clear about what you want to
calculate.
On Tue, Nov 23, 2010 at 1:27 AM, John S <s.john634.gmail.com> wrote:
> 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 Tue Nov 23 2010 - 06:00:03 PST
