Ho, first I minimize my structure. This is the corresponding mdp file: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz
and then I run a md run. This is the corresponding mdp file: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp = 200.0 gen_seed = 9999 constraints = all-bonds tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no In my topology file I include the restraint files like this: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif #ifdef POSRES #include "posre_memb.itp" #endif I just recognize that there is a "DPOSRES" in the mdp files and a "POSRES" in my topology file. Is this the problem. Do I have to write it the same way in the several files? Thank you > Hi, > > Did you call your genrestr output in your mdp file using define = * ? (for > example define = -DPOSRES ; where posres was your file name.) > > Thanks > > Peterson J > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/question-about-minimisation-tp4999681p4999685.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
