From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Thu Nov 25 2010 - 13:16:52 CST
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.
On Fri, Nov 26, 2010 at 3:04 AM, Sebastian Stolzenberg <
> Happy Thanksgiving, Joyce,
> it may be helpful, if you added the following to this namd thread:
> actual system size?
> What pressure outputs are you looking at?:
> GPRESSURE, PRESSURE with or without AVG?
> On 11/25/10 11:29 AM, Kwee Hong wrote:
>> I have my constant pressure control set as below during my equilibration
>> 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.
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