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-requ...@gromacs.org.
