[gmx-users] Virtual sites and diffusion coefficients.

sujithkakkat . sujithks58 at gmail.com
Tue Feb 3 08:04:48 CET 2015

Dear all,

     I tried simulating the CO2-water mixture with CO2 at a low
concentration (0.003 mole fraction) at various temperatures at 1 atmos.

I used the EPM2 parameters for the CO2 molecules which includes a flexible
OCO angle. I did a separate simulation on the similar system with CO2 model
constructed using virtual sites (following Justin Lemkul's tutorial) , with
the interaction parameters same as the EPM2 model.

In both cases the water model TIP4P was used.

I ran 5ns simulation after equilibrium was attained for the T and P values.

  When plotting the mean square displacement and fitting the graph to get
the diffusion coefficients, what I find is that the diffusion coefficient
obtained in the case of the CO2 model using virtual sites is much higher
(approximately two times) of that obtained for the EPM2 model without the
virtual sites.

  Let me know if any one came across this before. I would like to hear from
the more experienced users, what they think about this.

I will provide further details on the topology and MD parameters if



More information about the gromacs.org_gmx-users mailing list