Re: Constant pressure

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Thu Nov 25 2010 - 13:16:52 CST

Hi Sebastian,

Happy thanksgiving.

my .xsc is as below:

# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z
s_u s_v s_w
30000 42.9566 0 0 0 42.6204 0 0 0 42.3309 11.1618 -2.685 4.5548 -8.51178e-06
-8.51178e-06 -8.51178e-06 0 0 0

I was looking at the PRESSURE. Yet GPRESSURE and GPRESSUREAVG gives a
similar reading which fluctuates between -50 to 50 bar.

Joyce

On Fri, Nov 26, 2010 at 3:04 AM, Sebastian Stolzenberg <
s.stolzenberg_at_gmail.com> wrote:

> Happy Thanksgiving, Joyce,
>
> it may be helpful, if you added the following to this namd thread:
>
> 1.)
> actual system size?
> 2.)
> What pressure outputs are you looking at?:
> GPRESSURE, PRESSURE with or without AVG?
>
> Regards,
> Sebastian
>
>
> On 11/25/10 11:29 AM, Kwee Hong wrote:
>
>> Hi,
>>
>> I have my constant pressure control set as below during my equilibration
>> stage:
>>
>> useGroupPressure yes
>> useFlexibleCell no
>> useConstantArea no
>>
>> langevinPiston on
>>
>> langevinPistonTarget 1.01325
>> langevinPistonPeriod 100.
>> langevinPistonDecay 50.
>> langevinPistonTemp $temperature
>>
>> yet when I analyze my log file with NAMD plot, my pressure was found to
>> fluctuate between -300 bar and 300 bar. Is this normal?
>> When I read through the mailing list, someone says that this is caused by
>> small size of the system. And another comments fluctuation of plus minus 50
>> bar is normal.
>>
>> please advice and thannks in advance.
>>
>> Regards,
>> joyce
>>
>>
>>
>

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