Thank you Vedat!!! On Tue, Feb 28, 2012 at 8:35 PM, vedat durmaz <dur...@zib.de> wrote:
> ** > > hi jan/steven (?), > > you should know, in contrast to let's say justin lemkul, i haven't that > much experience with molecular simulations! > > actually, i don't expect large differences in conformational/statistical > properties depending on the usage of lincs constraints. usually i use them > when simulating target ligand systems with explicit solvent in order to > save time. for these large systems (in the order of 100,000 atoms), i set > emtol to about 300. > > however, for this small peptide (33AA) i refrained from constraints and > set emtol to 5 which is achieved quite quickly. for a large protein with > implicit solvent i would probably set emtol to 50 or something like that. > > > according to your strange results: > > i remember, i didn't do the energy minimization of the small peptide on > our computing cluster but on my local machine (six cpu-cores) with > gromacs-4.5.5 (no mpich, but openmpi). besides, i parameterized my peptide > using acpype (amber99sb force field) and didn't use editconf (didn't set > any box)! i just grompped the system and did the mdrun like > > grompp -f ../em.mdp -c ../peptide.pdb -p ../peptide.top -o em.tpr > mdrun -v -deffnm em > > and that's all .. 4 cores were used by mdrun. > > hope, that helps > > vedat > > > > > > Am 28.02.2012 17:56, schrieb Steven Neumann: > > I run energy minimization of my protein with implicit solvent: > > >> 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 = 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 = 2.25936 >> > > And I obtained: > > > Steepest Descents: > > Tolerance (Fmax) = 1.00000e+03 > > Number of steps = 30000 > > Step Time Lambda > > 0 0.00000 0.00000 > > Steepest Descents converged to Fmax < 1000 in 1 steps > > Potential Energy = inf > > Maximum force = 0.0000000e+00 on atom 0 > > Norm of force = nan > > > > Can you please explain? > > > > Steven > > On Tue, Feb 28, 2012 at 2:29 PM, Vedat Durmaz <dur...@zib.de> wrote: >> >>> actually, as far as i know, the -DFLEXIBLE argument has no effect on >>> simulations without explicit water ?! >>> >>> i just copied the "define" line from my explicit simulation systems .. >>> so, the only define value, that has a meaning is -DPOSRESHELIX. >>> >>> i didn't use constraints for the first time in my life since implicit >>> solvent simulations incorporate a much smaller number of atoms and are >>> therefore not that expensive computationally. i always use this setting for >>> my explicit simulations only in order to increase the step size to 2fs with >>> a clear conscience ... >>> >>> best wishes >>> vedat >>> >>> >>> Am 28.02.2012 15:18, schrieb Steven Neumann: >>> >>> 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 >>>>>>> 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 >>>>>> >>>>> >>>> -- >>>> ======================================== >>>> >>>> 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 <%28540%29%20231-9080> >>>> 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 >>>> 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 >
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