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On 15/06/2011 4:55 AM, Rini Gupta wrote:
<blockquote
cite="mid:1308019419.S.6489.7089.F.H.Tk1hcmsgQWJyYWhhbQBSZTogW2dteC11c2Vyc10gV2F0ZXIgUG90ZW50aWFsIEVuZXJneQ__.f4-235-144.1308077754.4488@webmail.rediffmail.com"
type="cite">Dear Mark,<br>
<br>
Thanks for the reply!<br>
<br>
I am using the same NPT conditions except time constants. <br>
The simulation was performed at constant temperature (300K) <br>
and pressure(1 bar) using velocity rescaling algorithm (tau=0.1
ps) <br>
for temperature coupling and Berendsen coupling <br>
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.<br>
Does it is making difference in calculated and reported values?<br>
</blockquote>
<br>
Maybe, but I'd randomly guess it would lead to a smaller difference
than that.<br>
<br>
<blockquote
cite="mid:1308019419.S.6489.7089.F.H.Tk1hcmsgQWJyYWhhbQBSZTogW2dteC11c2Vyc10gV2F0ZXIgUG90ZW50aWFsIEVuZXJneQ__.f4-235-144.1308077754.4488@webmail.rediffmail.com"
type="cite">
I am using LINCS algorithm to keep the geometries of all the
molecules <br>
rigid. Other conditions are exactly same.<br>
<br>
To see the size effect on the system,<br>
I have also done the same calculations with 8000 molecules but
result is same i.e. Water P.E=-46.7 kJ/mol.<br>
</blockquote>
<br>
I guess that means you are observing converged quantities. Maybe
they weren't observing such?<br>
<br>
There can also be differences in implementation between different
codes such that absolute energies are not necessarily comparable.
Energy differences should compare, however.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1308019419.S.6489.7089.F.H.Tk1hcmsgQWJyYWhhbQBSZTogW2dteC11c2Vyc10gV2F0ZXIgUG90ZW50aWFsIEVuZXJneQ__.f4-235-144.1308077754.4488@webmail.rediffmail.com"
type="cite">
Please clarify this issue.<br>
<br>
Best Regards,<br>
Rini<br>
<br>
On Tue, 14 Jun 2011 08:13:39 +0530 wrote<br>
>On 14/06/2011 4:18 AM, Rini Gupta wrote:<br>
<br>
> Dear gmx-users,<br>
<br>
><br>
<br>
> I am using GROMACS 4.5.4 to run a pure water system using
SPC/E model<br>
<br>
> containing 32000 molecules. I have done the equilibration for
2 ns <br>
<br>
> followed by production run of 5 ns using NPT ensemble at
300K.<br>
<br>
> I am using PME for treating electrostatic interactions
(cut-off 0.9 nm).<br>
<br>
> My question is Potential Energy of the system I am getting is
-46.7 <br>
<br>
> kJ/mol while literature value is -41.5 kJ/mol.<br>
<br>
> Can anyone please tell me why this discrepancy is coming?<br>
<br>
<br>
<br>
PE is size- and method-dependent. Are you reproducing the
conditions <br>
<br>
exactly?<br>
<br>
<br>
<br>
Mark<br>
<br>
-- <br>
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