AMBER Archive (2009)

Subject: Re: [AMBER] Box shape change

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jul 19 2009 - 08:51:44 CDT

Are you using any nonstandard force field? Is the temperature ok? You
might try to use taup of 0.1. Can't say much more without knowing the
details.

On Jul 19, 2009, at 8:05 AM, Hemant Kumar
<hemant_at_physics.iisc.ernet.in> wrote:

> 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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