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
> > 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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>
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Received on Fri Jan 28 2011 - 11:00:12 PST
