Re: Equilibration in NPT simulation

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Wed Jul 04 2018 - 11:30:50 CDT

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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