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 <[email protected]> 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 <[email protected]>wrote: >> >>> >>> >>> lina wrote: >>> >>>> On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann <[email protected]> >>>> 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 <[email protected]> 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 [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 >>>>> >>>> >>> -- >>> ======================================== >>> >>> 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 >>> >>> ======================================== >>> >>> -- >>> 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 >> > >
-- 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
