AMBER Archive (2009)

Subject: Re: [AMBER] Box shape change

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Jul 18 2009 - 20:35:41 CDT

What is the density? Did you equilibrate at NTP?

On Jul 18, 2009, at 3:38 PM, Hemant Kumar
<hemant_at_physics.iisc.ernet.in> wrote:

> Hi all,
> I am doing my simulation using pmemd with TIP3P as explicit solvent.
> My box shape seems to be distorted(no water mol at corners of box)
> starting from heating step(with ntb=1 and ntt=3 as well as ntt=1). I
> have tried various imaging options in ptraj like
> image origin center or image origin familiar
> but box looks same on vmd.
> distrotion continued during equilibration(NPT).
> Archive seems to suggest this is problem with imaging only. But for
> me it seems something else.
> Any suggestion will be appreciated.
> With regrads,
> Hemant Kumar
> Graduate Student
> CCMT,Department of Physics
> IISC,Bangalore
> URL www.physics.iisc.ernet.in/~hemant
>
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