Re: Re: [gmx-users] Water Potential Energy

[Rini Gupta]

Dear Mark,

 Thanks for the reply!

I am using the same NPT conditions except time constants. 
The simulation was performed at constant temperature (300K) 
and pressure(1 bar) using velocity rescaling algorithm (tau=0.1 ps) 
for temperature coupling and Berendsen coupling 
scheme (tau=1 ps) for pressure coupling whereas the in the references the system was coupled to bath of constant temperature (300K) and pressure (1 bar) using time constants tau=0.4 ps for temperature coupling and taup=0.4 ps for pressure coupling.
Does it is making difference in calculated and reported values?
I am using LINCS algorithm to keep the geometries of all the molecules 
rigid. Other conditions are exactly same.
 
To see the size effect on the system,
I have also done the same calculations with 8000 molecules but result is same i.e. Water P.E=-46.7 kJ/mol.

Please clarify this issue.

Best Regards,
Rini

On Tue, 14 Jun 2011 08:13:39 +0530  wrote
>On 14/06/2011 4:18 AM, Rini Gupta wrote:

> Dear gmx-users,

>

> I am using GROMACS 4.5.4 to run a pure water system using SPC/E model

> containing 32000 molecules. I have done the equilibration for 2 ns 

> followed by production run of 5 ns using NPT ensemble at 300K.

> I am using PME for treating electrostatic interactions (cut-off 0.9 nm).

> My question is Potential Energy of the system I am getting is -46.7 

> kJ/mol while literature value is -41.5 kJ/mol.

> Can anyone please tell me why this discrepancy is coming?



PE is size- and method-dependent. Are you reproducing the conditions 

exactly?



Mark

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