Hi all, I am running CGMD simulation of a membrane protein in DPPC with Martini FF.
I just want to check if these mdp files are correct. I would appreciate if you take a look and tell me if there is something wrong or missing.
<*minimization.mdp*> integrator = steep dt = 0.02 nsteps = 500 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout = 100 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein DPPC W_Ion tau-t = 1.0 1.0 1.0 ref-t = 300 300 300 define = -DPOSRES <*equilibration.mdp*> dt = 0.02 nsteps = 25000 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout = 100 xtc-precision = 100 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein DPPC W_Ion tau-t = 1.0 1.0 1.0 ref-t = 300 300 300 Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau-p = 12.0 12.0 compressibility = 3e-4 3e-4 ref-p = 1.0 1.0 refcoord_scaling = all <*md_2us.mdp*> dt = 0.02 nsteps = 100000000 nstxout = 0 nstvout = 0 nstlog = 10000 nstxtcout = 1000 xtc-precision = 100 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein DPPC W_Ion tau-t = 1.0 1.0 1.0 ref-t = 300 300 300 Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau-p = 12.0 12.0 compressibility = 3e-4 3e-4 ref-p = 1.0 1.0 Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c -- 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.
