What is the density? Did you equilibrate at NTP?
On Jul 18, 2009, at 3:38 PM, Hemant Kumar
<hemant.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
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> _______________________________________________
> 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
Received on Sun Jul 19 2009 - 01:07:12 PDT
