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

[Rasoul Nasiri]

On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:

> Note that two constrained atoms correspond to one constraint.
>
>


C12H26

26 constrained atoms due to hydrogens which have been connected to carbon
atoms.

Number of molecules 2550 therefore  66300 will be total constrained atoms
in cell.

> Cheers,
>
> T.
>


Rasoul



> 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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