Dear Justin, The following is from .mdf file.
; VARIOUS PREPROCESSING OPTIONS include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 22500000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1000 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 1 emstep = 0.01 ; Max number of iterations in relax_shells niter = 200 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 0 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 1000 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.22 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.22 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.22 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.26 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 1.0 ref_t = 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. gen_vel = yes gen_temp = 300 gen_seed = 1993 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = E-xt = E-y = E-yt = E-z = E-zt = ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 On Tue, Jan 5, 2016 at 2:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/5/16 2:51 PM, Chang Woon Jang wrote: > >> Dear Justin, >> >> Please take a look at the file. I modified mdp file provided from VOTCA >> tutorial. I think that mdp file is ok. >> >> > The mailing list does not accept attachments. Copy and paste the .mdp > contents. > > -Justin > > > Thank you very much. >> >> Best regards, >> Changwoon Jang >> >> On Tue, Jan 5, 2016 at 2:45 PM, Chang Woon Jang <changwoonj...@gmail.com> >> wrote: >> >> Dear Justin, >>> >>> Please take a look at the files. I modified mdp file provided from >>> VOTCA >>> tutorial. I think that mdp file is ok. >>> >>> I also attached full topology files as well. >>> >>> Thank you very much. >>> >>> Best regards, >>> Changwoon Jang >>> >>> >>> On Tue, Jan 5, 2016 at 2:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 1/5/16 2:25 PM, Chang Woon Jang wrote: >>>> >>>> Dear Justin, >>>>> >>>>> I am curious about resizing the box. My system contains 15000 >>>>> atoms >>>>> representing liquid polymer with very low density (maybe gas phase due >>>>> to >>>>> very low density). Does this very low density affect the simulation not >>>>> to >>>>> converge the box? Or, do the initial conditions (Pcoupl=berendsen, >>>>> Pcoupltype=isotropic, tau_p=5.0, compressibility=4.5e-5, ref_p=1.0) in >>>>> gromapp.mdp affect? Do I need to test these conditions? I am just >>>>> starting >>>>> to use GROMACS for obtaining atomistic trajectory compatible with VOTCA >>>>> coarse-graining package. >>>>> >>>>> >>>>> Those settings should be fine. Extract the box vectors from the .edr >>>> file and see how much they fluctuate; the final snapshot is not >>>> necessarily >>>> representative. But the fact that the box size is exactly the same from >>>> start to finish suggests there is something incorrect (or at least, >>>> really >>>> weird) going on. Provide the full text of your .mdp please, not just >>>> the >>>> section you think is relevant. >>>> >>>> -Justin >>>> >>>> >>>> The same configuration in LAMMPS works fine. >>>> >>>>> >>>>> Thank you. >>>>> >>>>> Best regards, >>>>> Changwoon Jang >>>>> >>>>> On Tue, Jan 5, 2016 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>> >>>>>> On 1/5/16 1:42 PM, Chang Woon Jang wrote: >>>>>> >>>>>> Dear Abhishek Khetan, >>>>>> >>>>>>> >>>>>>> Thank you for your answer. It means that Gromacs does not >>>>>>> automatically >>>>>>> adjust the box size even though NPT ensemble is employed. Am I right? >>>>>>> >>>>>>> >>>>>>> This is incorrect. The box size will change under the influence of >>>>>>> >>>>>> pressure. Its shape should be conserved. But if you're seeing the >>>>>> exact >>>>>> same box vectors before and after the simulation, something went wrong >>>>>> with >>>>>> your input. >>>>>> >>>>>> Different from Gromacs, Lammps automatically adjust box size when NPT >>>>>> >>>>>> ensemble is applied during the simulation. Therefore, the density is >>>>>>> able >>>>>>> to be fitted with initial conditions (pressure, temperature, >>>>>>> simulation >>>>>>> time). >>>>>>> >>>>>>> >>>>>>> GROMACS does this, too. >>>>>>> >>>>>> >>>>>> When I used the "gmx editconf" to resize the box to correct a density, >>>>>> vmd >>>>>> >>>>>> shows a very ugly configurations. I think that topology file will >>>>>>> check >>>>>>> the >>>>>>> bond informations no matter how the gro file, containing only atom >>>>>>> coordinates and box size, looks like. >>>>>>> >>>>>>> >>>>>>> Indeed, editconf is not useful here. It scales coordinate positions >>>>>>> to >>>>>>> >>>>>> achieve the desired density. This is not what you want. >>>>>> >>>>>> -Justin >>>>>> >>>>>> >>>>>> If I am wrong, please correct me. >>>>>> >>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> Best regards, >>>>>>> Changwoon Jang >>>>>>> >>>>>>> On Tue, Jan 5, 2016 at 1:16 PM, abhishek khetan <askhe...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>> To rescale the box.gro to a desired size using the actual density >>>>>>> 543.21 >>>>>>> >>>>>>> kg/l of the solvent and get a new scaled.gro file, I use this >>>>>>>> command: >>>>>>>> >>>>>>>> $ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang < >>>>>>>> changwoonj...@gmail.com >>>>>>>> >>>>>>>> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>> >>>>>>>> Dear Gromacs Users, >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> I have a low density polymer system initially. I would like to fit >>>>>>>>> the >>>>>>>>> correct liquid density using NPT simulation. >>>>>>>>> >>>>>>>>> I used Pcoupl=berendsen for 22 ns but the box size in confout.gro >>>>>>>>> is >>>>>>>>> >>>>>>>>> still >>>>>>>>> >>>>>>>> >>>>>>>> the same as the input size of conf.gro. >>>>>>>> >>>>>>>>> >>>>>>>>> Initial in conf.gro (10.0 10.0 9.8) >>>>>>>>> output in confout.gro (10.0 10.0 9.8) >>>>>>>>> >>>>>>>>> My initial conditions are >>>>>>>>> >>>>>>>>> tau_p=5.0 >>>>>>>>> compressibility=4.5e-5 >>>>>>>>> ref_p=1.0 >>>>>>>>> >>>>>>>>> Do I need to increase compressibility? >>>>>>>>> >>>>>>>>> Thank you. >>>>>>>>> >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> Changwoon Jang, >>>>>>>>> -- >>>>>>>>> Gromacs Users mailing list >>>>>>>>> >>>>>>>>> * Please search the archive at >>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>>>> posting! >>>>>>>>> >>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>>> >>>>>>>>> * For (un)subscribe requests visit >>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>>>> or >>>>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> || radhe radhe || >>>>>>>> >>>>>>>> abhishek >>>>>>>> -- >>>>>>>> Gromacs Users mailing list >>>>>>>> >>>>>>>> * Please search the archive at >>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>>> posting! >>>>>>>> >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>> >>>>>>>> * For (un)subscribe requests visit >>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>>> or >>>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>> ================================================== >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>>> >>>>>> Department of Pharmaceutical Sciences >>>>>> School of Pharmacy >>>>>> Health Sciences Facility II, Room 629 >>>>>> University of Maryland, Baltimore >>>>>> 20 Penn St. >>>>>> Baltimore, MD 21201 >>>>>> >>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>> http://mackerell.umaryland.edu/~jalemkul >>>>>> >>>>>> ================================================== >>>>>> >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to gmx-users-requ...@gromacs.org >>>>>> >>>>>> >>>>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 629 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>> http://mackerell.umaryland.edu/~jalemkul >>>> >>>> ================================================== >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> >>> >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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