On 6/07/2011 5:55 AM, Juliette N. wrote:
Hello Dear all,
I have a few short questions about pressure coupling settings, namely
isothermal compressibility. I hope you can guide me.
A) By default gmx is taking the value for water but I was wondering if
this has to be modified for other systems.
The compressibility value in the .mdp file can be chosen by you. See
discussion of P-coupling in the manual.
B) This quantity varies with T and P. so if I am to perform different
NPT runs ( different P runs), Do I have to put in corresponding
isothermal compress. for each pressure or it doesn't really matter?
(because it is of the order of 10^-5). Now I am using an average value
for the pressure range I am working with, which is about 3 times
higher than that of water.
Don't know. Get some 2nm water boxes and try it out :-)
C) Once NPT run is done, g_energy reports another isothermal
compressibility!. My question is if it takes this parameter as an
input what is the value g_energy is reporting? (although it seems what
gmx reports is not really accurate according to some of the posts in
the archive).
The observed compressibility, I suppose. It can be defined from other
observables. Note that the temperature coupling algorithm uses a
"temperature" and yet we make observations of temperature...
last Q) and my last question is about validity of OPLS-AA forcefiled
at high pressures. Could you please explain if employing oplsaa is
restricted to a certain pressure (or temperature) ? Does the accuracy
of results change from say 10 to 500 bar? I did not find any answer to
this question in the list archive.
Probably. Check out how it was parameterized and judge for yourself how
likely that performance will transfer to high pressure. Ultimately, you
have to be able to reproduce experimental data to suggest that such
transfer is valid.
Mark
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