Dear Justin, I use version 4.0.7
Thanks Afsaneh On 3/25/12, Justin A. Lemkul <[email protected]> wrote: > > > afsaneh maleki wrote: >> 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. >> > > Which Gromacs version are you using? I can't reproduce your problem with > version 4.5.4 or 4.5.5, either with or without the free energy code. My > energy > outputs are always present at the nstenergy interval. > > -Justin > >> >> 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 <[email protected]> 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 [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 >>> >> > > -- > ======================================== > > 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? 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