Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before.
title = production for ile-pro-SOL ; Run parameters integrator = sd ; leap-frog integrator nsteps = 1000000 ; 0.002* 1000000 = 2000 ps (2 ns) dt = 0.002 ; 2 fs tinit =0 ; Output control nstxout = 100000 ; save coordinates every 0.2 ps nstvout =100000 ; save velocities every 0.2 ps nstxtcout =100000 ; xtc compressed trajectory output every 2 ps nstenergy = 10000 ; save energies every 0.2 ps nstlog = 10000 ; update log file every 0.2 ps xtc_precision =1000 ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS unconstrained_start =no lincs_order =12 lincs_warnangle =30 shake-tol =0.0001 ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1.2 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths = rvdw-switch = 1. rvdw =1.1 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ; EWALD/PME/PPPM parameters = pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on ;tcoupl = Nose-Hoover ; More accurate thermostat ;pcoupl =Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ;restraints ;dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Peter C. Lai wrote: >> In the .mdp file what is nstenergy set to? >> > > I'd further ask what the rest of the .mdp file says, as well. If this is > the > output of energy minimization, it's totally normal. The output seems > irregular > but is due (I believe) to the potentially uneven step size taken during EM. > > -Justin > >> On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: >>> Dear users, >>> >>> >>> When I got "total energy.xvg" file for plotting total energy via time, >>> data haven't saved in order time intervals. What command can control >>> time intervals in .mdp for .edr file? To better understand I pasted >>> some text from "total energy.xvg" file. As you see, time intervals >>> aren't same. >>> >>> @ s0 legend "Total Energy" >>> 0.000000 -274454.750000 >>> 12.420001 -274884.187500 >>> 18.060001 -274532.343750 >>> 20.000000 -274475.437500 >>> 29.360001 -275739.562500 >>> 35.000000 -274441.937500 >>> 40.000000 -274463.156250 >>> 46.280003 -273342.250000 >>> 51.920002 -273099.718750 >>> 57.580002 -274429.250000 >>> 60.000004 -274844.062500 >>> 68.860001 -273905.093750 >>> 74.500000 -273988.812500 >>> 80.000000 -276057.625000 >>> >>> Thanks very much in advance >>> Afsaneh >>> -- >>> 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 > 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
