> > > On 6/12/12 7:34 AM, [email protected] wrote: >>> >>> >>> 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. > > There's nothing particularly special about running in vacuum except that > there > is no solvent. Infinite cutoffs and a nonperiodic simulation cell are > common > conventions for simulating in vacuum, so that's what the .mdp file above > does.
okey, thanks a lot!! But when I want to do a whole md run after this minimization my first .mdp file was correct, right? > > -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
