This box seems way too large. I'm assuming that the density is increasing
from 0.25.
It seems that you should create a new box in leap that is closer to the
actual size. Such a large box will probably take a very, very long time to
evolve down to the size it should be.
All the best,
Jason
On Fri, Jan 28, 2011 at 1:50 PM, John S <s.john634.gmail.com> wrote:
> The density is decreasing from 0.25 and it has not yet stabilized .After
> 100
> ps it reaches at 0.30 .
> Is it normal to have the solvent and polymer at the center of the box .
>
> Thanks
> John
>
> On Fri, Jan 28, 2011 at 11:14 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > What does the density look like? You should run equilibration at
> constant
> > pressure until the density stabilizes at the expected value (~1).
> >
> > Good luck!
> > Jason
> >
> > On Fri, Jan 28, 2011 at 11:13 AM, John S <s.john634.gmail.com> wrote:
> >
> > > Dear Amber Users,
> > >
> > > I made a solvate box using packmol with solvated polymer at center of
> box
> > > saved it as pdb file
> > >
> > > Then used xleap to make the box for the solvated polymer .
> > >
> > > x=loadpdb pm_sol.pdb
> > >
> > > set box x vdw 5
> > >
> > >
> > > I used constant volume minimization and then constant pressure dynamics
> > for
> > > 100 ps to equilibrate the box.Though this gives me no error,
> > >
> > > when I visualize my trajectory in VMD , here the box size is much
> larger
> > > and the contents are at the middle of the box .
> > >
> > > Should I continue with the constant pressure dynamics to have the box
> > size
> > > same as contents of the box , or equilibrate it till it attains the
> > usual
> > > density of the solvent at room temperature (as 1g/cc for water)
> > >
> > >
> > > Thanks
> > > John
> > > _______________________________________________
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> > > AMBER.ambermd.org
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jan 28 2011 - 11:00:14 PST
