[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

[Rasoul Nasiri]

On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Please just tell me how values of obtained T by g_traj can be corrected
> > when I use trajectory and tpr files of constrain MD simulations (OPLS) as
> > an input?
> >
>
>
> T(corrected) = T(g_traj)*natoms/(natoms-nconstraints)
>
>
T(g_traj)
 0      269.581
 1      271.064
 2      271.309
 3      271.205
 4      271.499
 5      270.868
 6      272.247
 7      271.59
 8      271.614
 9      270.598
 10     271.662

Corrected T based on the abovementione formula:

number of atoms : 96900
number of constarined atoms = 66300

Corrected T

 853.6732  858.3693  859.1452  858.8158  859.7468  857.7487  862.1155
860.035  860.111  856.8937  860.263

The desired temperature was 400K.






> Cheers,
>
> Tsjerk
>


Rasoul



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