Quoting Mark Abraham <mark.abra...@anu.edu.au>:
On 31/03/2010 5:19 AM, nishap.pa...@utoronto.ca wrote:
Hello,
I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My
simulations are 100ns each. I am using different cut-off. i.e
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0, 1.2 and 1.3
and these are my parameters for Pressure coupling":
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
Now after my simulations, when I use g_energy to extract average
pressure I get different values for all three cut-offs.
For the cut-off of 1.0nm, the average value doesn't converge to 1.0atm
but it is rather ~2.1atm, for 1.2cut off the avg. pressure is ~1.7 and
for 1.3cut off avg. pressure is ~1.03. I don't understand why the
pressure is not converging to 1.0atm for the cut-off of 1.0nm.. All the
parameters are exactly the same, the only difference between these
simulations are the cut-off values. Could anyone please give me some
insight on how the pressure coupling works and if this behaviour seems
normal?
You've not told us critical information, like the rest of your .mdp
file, or how you equilibrated before running your simulation from which
you collected data. You could be doing all sorts of weird things and we
simply couldn't know. Your electrostatic treatment is far more
significant than your use of rvdw.
Haphazardly changing simulation parameters is not a desirable thing to
do. Find a suitable model of physics in a published calculation,
evaluate its applicability to your situation, test its performance
suitably, and then apply it.
Mark
Thanks Mark, I will look into it and hopefully it will make more sense then.
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Nisha Patel
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