[gmx-users] conformational entropy with/without jumps
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Aug 19 15:43:14 CEST 2015
Hi Ahmet,
Have you looked at the trajectories? Is the molecule really whole/centered?
Cheers,
Tsjerk
T
On Wed, Aug 19, 2015 at 3:32 PM, Ahmet Yıldırım <ahmedo047 at gmail.com> wrote:
> Dear users,
>
> I am trying to get the conformational entropy of some structures but the
> results I got are strange. I tried two methods. I removed jumps from
> trajectory and centered the protein in box (1). I used the raw trajectory
> (2). GROMACS gives different results for each processes. Which trajectory
> should I use for the conformational entropy?
>
>
> For instance:
>
> 1) trajectory without jumps
>
> gmx trjconv -f md.xtc -s md.tpr -o traj-nojump.xtc -pbc nojump -b 30000
>
> gmx trjconv -f traj-nojump.xtc -s md.tpr -o traj-centered.xtc -pbc mol -ur
> compact -center
>
> gmx covar -f traj-centered.xtc -s md.tpr -b 30000
>
> gmx anaeig -f eigenvec.trr -entropy
>
> The Entropy due to the Quasi Harmonic approximation is 49621.05 J/mol K (I
> think this value is not physical)
>
>
> 2) raw trajectory
>
> gmx covar -f md.xtc -s md.tpr -b 30000
>
> gmx anaeig -f eigenvec.trr -entropy
>
> The Entropy due to the Quasi Harmonic approximation is 2633.88 J/mol K
>
>
> I did some tests on GROMACS 5.0.4 and GROMACS 5.0.6.
>
>
> --
> Ahmet Yıldırım
> --
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--
Tsjerk A. Wassenaar, Ph.D.
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