[gmx-users] conformational entropy with/without jumps

[Ahmet Yıldırım]

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.


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