From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Thu Dec 02 2010 - 10:46:45 CST
Thank you for your help, JÃ©rÃ´me,
> but hopefully our friends in Urbana will chime in.
Any news from our friends in Urbana?
In particular, I wonder why "UseGroupPressure" is "no" as default.
On 11/29/10 11:26 AM, JÃ©rÃ´me HÃ©nin wrote:
> Dear Sebastian,
> On 26 November 2010 20:03, Sebastian Stolzenberg
> <s.stolzenberg_at_gmail.com> wrote:
>> Dear Jerome,
>>> It does sound like a problem. To distinguish whether it comes from
>>> pressure measurement itself or from the barostat, it would be very
>>> useful to repeat this comparative test in constant volume simulations.
>> To achieve running an NVT ensemble simulation, I did the following:
>> - switch off the "LangevinPiston" options
>> - useFlexibleCell "yes"->"no"
>> I have four runs of the same system:
>> a) with piston (NPT), group pressure yes
>> b) with piston (NPT), group pressure no
>> c) NVT, group pressure yes
>> d) NVT, group pressure no
>> with the following mean GPRESSAVG values:
>> a) (1.1+-1.6)bar
>> b) (-14.1+-2.6)bar
>> c) (8.8+-12.8)bar
>> d) (-0.94+-13.01)bar
>> means are over>=0.5ns trajectories. Uncertainties are simple standard
>> deviations (energy fluctuations are numerically too large to compute
>> Boltzmann averages).
>> My Questions:
>> Does this help at all? If yes, please explain: are you simply looking for
>> differences in the GPRESSAVG output?
>> Or are there distinct pressure values/differences in the NVT that I would
>> have to expect physically?
> These results (which match what I have just measured on a simple cubic
> water box) indicate that the root of the issue is not a problem with
> the barostat. Still, it suggests that the barostat might not be using
> the same pressure value as the one in the output when useGroupPressure
> is disabled, as it fails to bring that value to 1 bar.
>> 2.) As a consequence, is it safer to use GroupPressure, even if the "rigidBonds"
>> option is not used?
> That would seem to be the case, although I would not use the word
> "safe" until this surprising behavior is fully sorted out. I am not
> well-versed in that part of the code (especially since the dreaded
> ComputeNonBondedBase(2).h might be involved), but hopefully our
> friends in Urbana will chime in.
>> Qu'est-ce que c'est, je ne trouve pas "FÄ™te de la rÃ©colte" en wikipedia pour
>> la France!
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