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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Received on Fri Jan 28 2011 - 08:30:12 PST
