When you go to NPT, the box is shrunk to equilibrate
the pressure. This is done by scaling all the coordinates,
so the contents of the box seem to drift toward the origin.
It looks a bit eerie when the waters are not visualized
because the solute just floats over and stops.
As this happens, the bond potential and shake correct the
shrinkage within each molecule. When pressure has equilibrated,
it stops.
Bill
> By drifting I mean the system as a whole has a
> movement
> in a direction during the heating from 293K to 300 at
> constant pressure. (I think the center of mass has a
> velocity in a particular direction). After 10ps, the
> system attains 300K and after that there is no such
> movement.
>
> --- Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
> wrote:
>
> > what do you mean by the "nucleic acid is drifted"?
> > you'll need to be much more specific. Also check the
> > archives and read the manual about imaging in case
> > that
> > is the problem.
> >
> > mathew k varghese wrote:
> >
> > >Dear AMBER users,
> > >
> > >
> > >I am runnig MD simulation of a nucleic acid in
> > >explicit solvent. In the first step of
> > equillibration
> > >the system is heated to 300K(actual final
> > temperature
> > >attained is 293.18K)at constant VOLUME in 50ps. In
> > the
> > >next step the run was in constant PRESSURE and I
> > >heated the system in 10ps from 293.18 to 300 and
> > then
> > >40ps at 300 k.
> > >When the trajectory is viewed, during the 10ps
> > heating
> > >from 293.18 to 300 at constant pressure the nucleic
> > >acid is drifted. Is it normal? If not how can I
> > >correct this?
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Received on Fri Sep 09 2005 - 15:53:01 PDT
