I will try that out.
Thanks
On Fri, Jan 28, 2011 at 1:54 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
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> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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Received on Fri Jan 28 2011 - 13:00:02 PST
