Re: Set up NPT simulation in cubic PBC-box

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 27 2012 - 11:11:30 CDT

On Fri, Apr 27, 2012 at 12:08 PM, Xi Cheng <xichengeva_at_gmail.com> wrote:
> Hi Axel,
>
> According to the description of "useFlexibleCell", if it is set to be "yes", then NAMD allows the three orthogonal dimensions of the periodic cell to fluctuate independently.
>
> What will happen, if I set it to be "no"?

have you tried it? only takes a few minutes to
know whether it works when running a small
test system.

> The three orthogonal dimensions of the periodic cell will not fluctuate?
> Or they will fluctuate dependently?

just re-read that segment again and think about
the logic and then find the answer yourself. this will
help you to solve similar problems in the future.

axel.

> It is important for my NPT simulation.
>
> Thanks,
> Xi
>
>
> On Apr 27, 2012, at 10:54 AM, Axel Kohlmeyer wrote:
>
>> On Thu, Apr 26, 2012 at 5:22 PM, Xi Cheng <xichengeva_at_gmail.com> wrote:
>>> Hi,
>>>
>>> Is it possible to allow the three orthogonal dimensions of the periodic cell
>>> to fluctuate
>>> and keep the ratio of the unit cell in x-y/y-z/z-x plane constant at the
>>> same time?
>>>
>>> Or is there any other way to run NPT simulation in cubic PBC box?
>>
>> it should get it, if you keep the default settings, i.e.
>>
>> useFlexibleCell no
>> useConstantArea no
>> useConstantRatio no
>>
>> at least that is what the documentation indicates.
>>
>> axel.
>>
>>
>>>
>>> Thanks,
>>> Xi
>>>
>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:28 CST