AMBER Archive (2009)

Subject: Re: [AMBER] Box shape change

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jul 19 2009 - 06:40:03 CDT

200ps may be short- what was your pressure coupling constant?
sounds like your box has vacuum bubbles.

On Sun, Jul 19, 2009 at 7:00 AM, Hemant Kumar
<hemant_at_physics.iisc.ernet.in>wrote:

> 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<http://www.physics.iisc.ernet.in/%7Ehemant>
>
> 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<http://www.physics.iisc.ernet.in/%7Ehemant>
>>>
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