Thank you all! How about -DFLEXIBLE in both em and md?
Steven On Tue, Feb 28, 2012 at 2:13 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > lina wrote: > >> 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. >> >> > A system that is unstable will cause the LINCS algorithm to fail, but > turning off constraints does not prevent a system from becoming unstable or > crashing. > > -Justin > > > 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<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<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> >>> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > 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> >
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