[gmx-users] Rigid water model

[Michael Shirts]

Setting the compressibility in gromacs actually is just as way adjust the stiffness of the barostat. 

Berendsen thermostat guarantees a Cp that is too low. Try v-rescale or nose-Hoover.

See http://pubs.acs.org/doi/abs/10.1021/ct300688p

For more info.

Sent from my iPhone

> On Mar 16, 2014, at 8:33, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
>> On Mar 14, 2014 11:06 PM, "Michelle Aranha" <maranha at utk.edu> wrote:
>> 
>> Hi!
>> I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3
>> density, 10 ns NPT simulation (298 K & 1 bar)with Parinello Rahman
> Barostat
>> and Berendsen thermostat.
> 
> Using a thermostat that produces the wrong velocity distribution is asking
> for trouble. No idea if that's your main problem, though.
> 
>> Here is my result for SPC water
>> 
>> Kappa (J/m3)    5.689E-10
>> Cp      22.8054
>> Cp- Cv  5.94102
>> 
>> The density, diffusion coefficient, the average configuration energy agree
>> with previous results. However the heat capacity value is quite low as
>> compared to 75 J/mol K of real water or even that has been previously
> found
>> with water models. I compared my values with a 2 ns and 10 ns simulations,
>> but the heat capacity value shows no real improvement. I do not know much
>> about quantum corrections hence I have not tried it. Will applying quantum
>> corrections give the correct heat capacity?
>> The isothermal compressibility  reported by GROMACS is in J/m3 and the
>> adiabatic bulk modulus is reported in m^3/J, could that be a mistake and
>> should it be rather in  (J/m^3)^-1 and J/m3 respectively.
>> And, why does the isothermal compressibility change during the course of
>> simulation if it has been fixed in the mdp file.
> 
> A parameter for an algorithm and an observed property are two different
> things!
> 
> Mark
> 
>> 
>> Best wishes,
>> Michelle
>> 
>> 
>> --
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>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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