On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann <s.neuman...@gmail.com> wrote: > Thank you Vedat! > > Why do you use -DFLEXIBLE in md and in em? > Why dont you use constraint algorithm (LINCS) in your simulation?
Otherwise, the system is easily explode with lots of LINCS warning. Also thanks Vedat for sharing, Best regards, > > Steven > > On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz <dur...@zib.de> wrote: >> >> >> hi steven, >> >> i've been simulating a 33 AA peptide for the past two days using implicent >> solvent in order to achieve a proper folding. >> >> i haven't added counterions, however, the systems shows nice results >> according to what i've expected. the mdrun command (for the extension) for >> our hardware looks as follows: >> >> mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt -deffnm md 2>&1 >> >> and here's the mdp file for the energy minimization: >> >> define = -DFLEXIBLE >> constraints = none >> integrator = steep >> dt = 0.001 ; ps >> nsteps = 30000 >> vdwtype = cut-off >> coulombtype = cut-off >> pbc = no >> nstlist = 0 >> ns_type = simple >> rlist = 0 ; this means all-vs-all (no cut-off), which >> gets expensive for bigger systems >> rcoulomb = 0 >> rvdw = 0 >> comm-mode = angular >> comm-grps = Protein >> optimize_fft = yes >> ; >> ; Energy minimizing stuff >> ; >> emtol = 5.0 >> emstep = 0.01 >> ; >> ; Implicit solvent >> ; >> implicit_solvent = GBSA >> gb_algorithm = Still ; HCT ; OBC >> nstgbradii = 1 >> rgbradii = 0 ; [nm] Cut-off for the calculation of the Born >> radii. Currently must be equal to rlist >> gb_epsilon_solvent = 80 ; Dielectric constant for the implicit >> solvent >> ; gb_saltconc = 0 ; Salt concentration for implicit solvent >> models, currently not used >> sa_algorithm = Ace-approximation >> sa_surface_tension = -1 >> >> >> and for the md run: >> >> define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES >> constraints = none >> integrator = md >> dt = 0.001 ; ps >> nsteps = 1000000000 ; 100000 ps = 100 ns >> nstcomm = 10 >> nstcalcenergy = 10 >> nstxout = 1000 ; frequency to write coordinates to output >> trajectory >> nstvout = 0 ; frequency to write velocities to output >> trajectory; the last velocities are always written >> nstfout = 0 ; frequency to write forces to output >> trajectory >> nstlog = 1000 ; frequency to write energies to log >> file >> nstenergy = 1000 ; frequency to write energies to edr file >> >> vdwtype = cut-off >> coulombtype = cut-off >> >> pbc = no >> >> nstlist = 0 >> ns_type = simple >> rlist = 0 ; this means all-vs-all (no cut-off), which >> gets expensive for bigger systems >> rcoulomb = 0 >> rvdw = 0 >> >> comm-mode = angular >> comm-grps = system >> >> optimize_fft = yes >> >> ; V-rescale temperature coupling is on >> Tcoupl = v-rescale >> tau_t = 0.1 >> tc_grps = system >> ref_t = 300 >> ; Pressure coupling is off >> Pcoupl = no >> ; Generate velocites is on >> gen_vel = yes >> gen_temp = 300 >> gen_seed = -1 >> >> ; >> ; Implicit solvent >> ; >> implicit_solvent = GBSA >> gb_algorithm = Still ; HCT ; OBC >> nstgbradii = 1 >> rgbradii = 0 ; [nm] Cut-off for the calculation of the Born >> radii. Currently must be equal to rlist >> gb_epsilon_solvent = 80 ; Dielectric constant for the implicit >> solvent >> ; gb_saltconc = 0 ; Salt concentration for implicit solvent >> models, currently not used >> sa_algorithm = Ace-approximation >> sa_surface_tension = -1 >> >> >> best regards, >> vedat >> >> >> Am 28.02.2012 11:59, schrieb Steven Neumann: >> >>> Dear Gmx Users, >>> I am using Gromacs 4.5.4 and I would like to implement implicit solvent >>> for folding of my protein. I read mailing list and it is still confusing for >>> me. >>> Is it proper to use counterions within the system? If not, how can I >>> obtain netral system? >>> Do we use cut off for vdw and coulombic interactions? >>> What kind of integrator should be used with a timestep? >>> I will appreciate an mdp file for protein folding! Thank you >>> Steven >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
