> On 26/07/2012 6:47 PM, [email protected] wrote: >> 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 > > This won't work for multiple [moleculetype] entries. See > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > >> >> >> 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? > > http://www.gromacs.org/Documentation/Include_File_Mechanism > > Mark
I just see that the [ position_restraints ] part is included under the [dihedral] and not between the [moleculetype] and the [atom] part. And according to the site you wrote me this is a problem, right? But this was done by gromacs itself. Shell I write it to the [moleculetype] part? But I can not see why it can not work that I have 2 restriction files? Can you please explain it to me? So you mean that it is indeed important if I call it POSRES oder DPOSRES, right? Thank you > >> >> 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 > -- 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
