Re: Equilibration in NPT simulation

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Jul 04 2018 - 13:37:31 CDT

Looking at any single value of the pressure will not be informative due to
the very high expected variance in the instantaneous pressure. See the
discussion at the top of
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node37.html
Once you have run constant pressure equilibration for long enough that the
unit cell size stabilizes, the average of the pressure over a decent number
of samples should approach your target value.

Best,
Peter

On Wed, Jul 4, 2018 at 12:59 PM, Mani Kandan <manikandand5110_at_gmail.com>
wrote:

> I am having all 4 pressure values in positive sign and values are high (ex
> one time output : 2519186.3001 2519187.5205 2518108.1341 2518107.9413).
> Then definitely my average should be in the same range. Then how can i get
> my target pressure 1.03125 bar?
>
> Manikandan
>
> On Wed, Jul 4, 2018 at 10:00 PM, Mani Kandan <manikandand5110_at_gmail.com>
> wrote:
>
>> Thanks,
>>
>> What about the values of Pxx,Pxy,Pxz,Pyx,Pyy,Pyz,Pzx,Pzy,Pzz?
>>
>> If I am fixing some atoms in my simulation, then is it will affect my
>> pressure calculation?
>>
>>
>>
>> On Wed, Jul 4, 2018 at 9:16 PM, Kowsar Khajeh <khajeh.k.2005_at_gmail.com>
>> wrote:
>>
>>> Hello.
>>> In log file, we have 4types of pressure (GPressAvg,GPress,...). These
>>> data are for each time step. You can extract these data by using different
>>> comments in Linux (for exam; awk comment). After that, if you do average
>>> you will get the mean pressure.
>>> Best
>>>
>>>
>>>
>>> On Thu, Jul 5, 2018, 12:26 AM Mani Kandan <manikandand5110_at_gmail.com>
>>> wrote:
>>>
>>>> Dear All,
>>>>
>>>> For NPT simulation, I am using Langevin dynamics in
>>>> namd and parameters are given below
>>>> useGroupPressure on
>>>> useFlexibleCell yes
>>>> useConstantArea yes
>>>> langevinPiston on
>>>> langevinPistonTarget 1.01325
>>>> langevinPistonTemp 300
>>>> langevinPistonDecay 300
>>>> langevinPistonPeriod 300
>>>>
>>>> How can I check, If my system reached 1.01325 bar or not? since output
>>>> pressure has many values. Kindly help me in this.
>>>>
>>>>
>>>> Manikandan
>>>>
>>>
>>
>

This archive was generated by hypermail 2.1.6 : Sun Sep 15 2019 - 23:19:48 CDT