Hi all, Could someone please help me? I have a question about the *temperature outputs *from the two packages "gmx traj" and "gmx energy."
I used the two packages to export the Temperature of a "Protein" group. Here is what I did. 1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot Temperature_traj.xvg gmx analyze -f Temperature_traj.xvg *Found: Temperature_traj = 250.475 K* 2. gmx energy -f energy.edr Select "14 Temperature". *Found: Temperature_energy = 300.137 K* Our *parameters.mdp* file has: "... constraints = h-bonds constraint_algorithm = Lincs tc-grps = System ; sd integrator (!) tau_t = 2.0 ; sd integrator (!) ref_t = 300 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ..." I don't know why the two temperatures are that much different from each other, such as by 50 degrees. Looking forward to an explanation. Thanks a lot. Sincerely yours, Anh Mai -- 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.
