From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Dec 18 2014 - 13:17:35 CST
Hi Shalton,
You'll need to also set other options as well, specifically turning on
one of the two algorithms that implement pressure control (either
Berendsen or Langevin). Read the user guide section for all the details
as to what the options are
(http://www.ks.uiuc.edu/Research/namd/2.10/ug/node37.html), and think
carefully about what options you'd like.
To get you started, here is a section from a simulation I ran of a
waterbox, which sounds like it would be similar to your case.
useFlexibleCell no ; # If its just a liquid box, you expect
isotropic box size fluctuations
langevinPiston on
langevinPistonTarget 1.01325 ; #Atmospheric pressure
langevinPistonPeriod 200
langevinPistonDecay 200
langevinPistonTemp $temperature
The volume won't change during minimization, but this will get you
variations in volume during equilibration.
-Josh Vermaas
On 12/18/2014 01:01 PM, Miss. State wrote:
>> Hello All,
>>
>> I'm trying to perform a minimization and equilibration on a liquid mixture of propylene carbonate and ethylene carbonate. I'm trying to do this first with variable volume, fixing temperature and pressure. And, then thereafter, minimize with variable pressure, fixing temperature and volume. I tried using the Constant Pressure Control options; useGroupPressure and useFlexibleCell. When enabling both of these, the namdplot shows a constant volume and variable pressure. I don't understand what is going on here but I would expect a variable volume and constant pressure. Some help/advice on this matter would be appreciated. Attached is a print screen of the namdplot.
>>
>> Shalton Evans
>>
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