Re: Equilibration in NPT simulation

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Wed Jul 04 2018 - 11:59:38 CDT

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
>>>
>>
>

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