AMBER Archive (2009)

Subject: [AMBER] Box shape change

From: Hemant Kumar (hemant_at_physics.iisc.ernet.in)
Date: Sat Jul 18 2009 - 14:38:46 CDT

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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