> On 13/06/2012 5:59 PM, [email protected] wrote: >> Hi, >> I want to do a MD simulation in vacuum. > > So don't turn on implicit solvent. Sorry, my fault. I want to do it in implicit solvent. > >> So first I wanted to prepare the >> files for that with "grompp". >> But there I got the error that >> "With GBSA implicit solvent, rgbradii must be equal to rlist" >> >> But the 2 values are the same in my .mdp file. Can you please show me >> where the failure is? >> >> >> define = -DPOSRES >> integrator = md >> emtol = 1000.0 >> emstep = 0.01 >> nsteps = 50000 >> nstlist = 1 >> ns_type = simple >> rgbradii = 0 >> rlist = 0 >> coulombtype = cutoff >> vdwtype = cutoff > > These are misspelled. > > See manual 7.3.9 for how to simulate without cut-offs. > > Mark > >> rcoulomb = 0 >> rvdw = 0 >> pbc = no >> epsilon_rf = 0 >> >> implicit_solvent = GBSA >> gb_algorithm = HCT >> gb_epsilon_solvent = 78.3 >> >> nstxout = 1 >> nstfout = 1 >> nstvout = 1 >> nstxtcout = 1 >> nstlog = 1 >> >> >> >> Thank you, >> Eva >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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 >
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