Thank you Vedat! Why do you use -DFLEXIBLE in md and in em? Why dont you use constraint algorithm (LINCS) in your simulation?
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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
