[gmx-users] Water Potential Energy

[Mark Abraham]

On 15/06/2011 4:55 AM, Rini Gupta wrote:
> 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?

Maybe, but I'd randomly guess it would lead to a smaller difference than 
that.

> 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.

I guess that means you are observing converged quantities. Maybe they 
weren't observing such?

There can also be differences in implementation between different codes 
such that absolute energies are not necessarily comparable. Energy 
differences should compare, however.

Mark

> 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
>
> -- 
>
> gmx-users mailing list gmx-users at gromacs.org
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
>
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
> Please don't post (un)subscribe requests to the list. Use the
>
> www interface or send it to gmx-users-request at gromacs.org.
>
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?> 
>
>
>
> Treat yourself at a restaurant, spa, resort and much more with *Rediff 
> Deal ho jaye! 
> <http://track.rediff.com/click?url=___http://dealhojaye.rediff.com?sc_cid=mailsignature___&cmp=signature&lnk=rediffmailsignature&newservice=deals>* 


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110615/d4adb353/attachment.html>