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

[Tsjerk Wassenaar]

Note that two constrained atoms correspond to one constraint.

Cheers,

T.
On Jul 12, 2014 12:01 PM, "Rasoul Nasiri" <nasiri1355 at gmail.com> wrote:

> 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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