> > > On 6/12/12 7:46 AM, [email protected] wrote: >>> >>> >>> 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? >> > > For running in implicit solvent, that .mdp file has a number of problems. > > By restraining the protein, you don't really accomplish anything. Also > note > that for using implicit solvent, you generally need infinite cutoffs (like > in > the case of the "vacuum" .mdp file I posted before) and no pressure > coupling. I > have found that with finite cutoffs, energy conservation is poor and > structures > are unstable when using implicit solvent. > > There are a number of useful discussions in the list archive about such > considerations; I would encourage you to spend some time reading before > diving > headfirst into something that may not turn out well.
But when I want only the water atoms to be minimized and to run the md simulation only for the water atoms I have to restrain the whole protein or not? I already googled around a lot and I found many many examples for .mdp files. Is it possible to run an md simulation with the following .mpd file? define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = -1 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = cut-off vdwtype = cut-off rcoulomb = 1.0 rvdw = 1.0 pbc = no epsilon_rf = 0 rgbradii = 1.0 comm_mode = angular implicit_solvent = GBSA gb_algorithm = HCT gb_epsilon_solvent = 78.3 sa_surface_tension = 2.25936 nstxout = 0 nstfout = 0 nstvout = 0 nstxtcout = 0 nstlog = 0 nstcalcenergy = -1 nstenergy = 0 tcoupl = berendsen tc-grps = system tau-t = 0.1 ref-t = 300 Eva > > -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
