To be more clear ,I am calculating as below,
trajin md.x 4 40000 4
strip :64-200 (here i remove the solvent)
rms first mass :1-63
trajout md_1ps.x
diffusion :1 1 res1
diffusion :2 1 res2
or I should do
trjain md.x 4 40000 4
strip :64-200
diffusion :1 1 res1
diffusion :2 1 res2
I am using the md_1ps.x trajectory for my calculation like normal mode
analysis, visualization and binding energy .
Thanks
John
On Tue, Nov 23, 2010 at 8:43 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 11:30:05 PST
