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 -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
