[gmx-users] conformational entropy with/without jumps

[Tsjerk Wassenaar]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.




-- 
Tsjerk A. Wassenaar, Ph.D.