Hi, I have obtained a 100 ns simulation using Amber. I would like to calculate the potential energy (VDW, COUL,ect) from the trajectory, below is my command.
$gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o rerun.tpr -maxwarn 1 $gmx mdrun -rerun ../protein.trr -s rerun.tpr -g rerun.log -e rerun.edr $gmx energy -f rerun.edr -o test.xvg My question is: in this test.mdp file, should I specify any parameters that should be the same as I used when running MD using Amber. Run parameters integrator = md nsteps = 500000 ; dt = 0.002 ; 2 fs ; Output control nstxout = 10000 ; nstvout = 10000 ; nstfout = 0 ; nstxtcout = 1000 ; ;nstxout-compressed = 1000 ; nstenergy = 1000 ; nstlog = 10000 ; ; Constraints constraint_algorithm = lincs ; constraints = hbonds ; d lincs_iter = 1 ; lincs_order = 4 ; continuation = yes ; ; Neighborsearching cutoff-scheme = Verlet ; verlet-buffer-tolerance = 0.005 ; ns_type = grid ; nstlist = 20 ; rlist = 1.0 ; rcoulomb = 1.0 ; rvdw = 1.0 ; ; Electrostatics coulombtype = PME ; pme_order = 4 ; fourierspacing = 0.16 ; ; Temperature coupling is on tcoupl = V-rescale ; tc-grps = System ; tau_t = 0.1 ; ref_t = 300 ; pcoupl = Parrinello-Rahman ; pcoupltype = isotropic ; tau_p = 2.0 ; ref_p = 1.0 ; compressibility = 4.5e-5 ; pbc = xyz ; DispCorr = EnerPres ; gen_vel = no pull = no -- 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.