AMBER Archive (2009)

Subject: Re: [AMBER] Box shape change

From: Hemant Kumar (hemant_at_physics.iisc.ernet.in)
Date: Sun Jul 19 2009 - 07:05:04 CDT

Hi Carlos,
Thanks for your quick reply.
Value of taup=0.5,during equilibration as well as production
I am running my production in NTP, so distortion continues in production
run as well.so I don't think it is short equilibration problem.
I have kept solvation layer of 15A in all directions, this may cause
problem.
To remove vacuum bubbles,should I run NVT step longer?
One more thing, I am keeping my solute fixed during all my
simulation(except minimization).

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

On Sun, 19 Jul 2009, Carlos Simmerling wrote:

> 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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