My system consists of CNT bundle solvated in TIP3P water.
I am using AMBER03 force field.
I had sucessfully completed my simulation with single CNT using same
procedure. Problem arises only when I switch to CNT bundle.
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.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.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>
>>>>
>>>> --
>>>> This message has been scanned for viruses and
>>>> dangerous content by MailScanner, and is
>>>> believed to be clean.
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 19 2009 - 18:07:16 PDT
