AMBER Archive (2009)

Subject: Re: [AMBER] Box shape change

From: Hemant Kumar (hemant_at_physics.iisc.ernet.in)
Date: Sun Jul 19 2009 - 06:00:18 CDT

After heating in NVT ,I equilibrated for 200ps in NPT.
Density of my system equilibrates at 0.89.

With regrads,
Hemant Kumar
Graduate Student
CCMT,Department of Physics
IISC,Bangalore
URL www.physics.iisc.ernet.in/~hemant

On Sat, 18 Jul 2009, Carlos Simmerling wrote:

> 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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