> > > On 6/12/12 7:05 AM, [email protected] wrote: >>> >>> >>> On 6/12/12 5:54 AM, [email protected] wrote: >>>> Hi everybody, >>>> I tried to run a minimization just of the hydrogen of a membrane >>>> protein. >>>> I want to do this in vacuum. >>>> >>>> But when I started the run with >>>> >>>> mpirun mdrun_mpi -deffnm protein -v -nt 2 >>>> >>>> I get the error that there is a segmentation fault. >>> >>> Threading and MPI parallelization are independent. You can't use both. >>> If >>> you've compiled with MPI support, you can't invoke the -nt option. >> >> okey, I'll try it without the -nt option. But I still get the error >>> >>>> But when I only type >>>> >>>> mpirun mdrun_mpi >>>> >>>> there is no problem so I guess that my already produced input files >>>> are >>>> the problem. For example I am not completely sure about the .mdp file. >>>> Can >>>> you please give me an example for a .mdp file for a minimization of >>>> only >>>> the hydrogen but not the whole protein in a vacuum. >>>> >>> >>> It would be far more useful for you to post what you're using so we can >>> provide >> >> >> The .mpd file I use looks like this: >> >> define = -DPOSRES >> integrator = md >> tinit = 0 >> dt = 0.005 >> nsteps = 20000 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 0 >> nstlog = 1000 >> nstxtcout = 1000 >> nstenergy = 1000 >> energygrps = Protein Non-Protein >> nstcalcenergy = 5 >> nstlist = 5 >> ns-type = Grid >> pbc = xyz >> rlist = 0.9 >> coulombtype = Cut-off >> rcoulomb = 0.9 >> rvdw = 0.9 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> tcoupl = V-rescale >> tc-grps = Protein Non-Protein >> tau_t = 0.1 0.1 >> ref_t = 298 298 >> Pcoupltype = Isotropic >> tau_p = 2.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> gen_vel = no >> constraints = all-bonds >> constraint-algorithm = Lincs >> unconstrained-start = yes >> lincs-order = 4 >> lincs-iter = 1 >> lincs-warnangle = 30 >> implicit_solvent = GBSA >> gb_algorithm = HCT >> nstgbradii = 1.0 >> rgbradii = 0.9 >> gb_epsilon_solvent = 80 >> gb_dielectric_offset = 0.009 >> sa_algorithm = Ace-approximation >> > > Your goal is energy minimization of H atoms in a vacuum, correct? Your > .mdp > file is for a full MD simulation using an NVT ensemble in implicit > solvent. > What you want is something more along the lines of: > > define = -DPOSRES > integrator = steep > emtol = 1000.0 > emstep = 0.01 > nsteps = 50000 > energygrps = system > nstlist = 1 > ns_type = simple > rlist = 0 > coulombtype = cutoff > rcoulomb = 0 > rvdw = 0 > pbc = no
but how does the minimization "know" that it should be in vacuum. > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > 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 > -- 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
