[gmx-users] Pressure average problem

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Tue Mar 30 22:44:28 CEST 2010

Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:

> On 31/03/2010 5:19 AM, nishap.patel at 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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