[gmx-users] Virtual sites and diffusion coefficients.

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 3 09:10:52 CET 2015


With which set of parameters are you able to reproduce the original
parametrization results?


On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . <sujithks58 at gmail.com> wrote:

> 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
> necessary.
> Regards,
> Sujith.
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