On Fri, Aug 20, 2021, 16:08 Satyen Dhamankar <[email protected]> wrote:
> You are right, Christoph. I did end up catching that error... However, I > am now facing an issue with energygroups. > > PNM in energygrp-table is not an energy group > > Did you run make_index to create all these energy groups? Christoph > > > This is my mdp file: > ``` > ; RUN CONTROL PARAMETERS > integrator = sd > ; Start time and timestep in ps > tinit = 0 > dt = 0.004 > nsteps = 1000000 > ; 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 = 1 > ; group(s) for center of mass motion removal > comm-grps = > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) and fo_ces (f) > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Output frequency for energies to log file and energy file > nstlog = 0 > nstenergy = 5000 > ; Output frequency and precision for xtc file > nstxout-compressed = 100 > compressed-x-precision = 1000 > ; Selection of energy groups > energygrps = WT PNM_&_BB PNM_&_BA PNM_&_BI > > ; NEIGHBORSEARCHING PARAMETERS > ; nblist update frequency > nstlist = 5 > ; ns algorithm (simple or grid) > ns-type = Grid > ; Periodic boundary conditions: xyz, no, xy > pbc = xyz > periodic_molecules = no > ; nblist cut-off > rlist = 1.4 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = User > rcoulomb-switch = 0 > rcoulomb = 1.4 > ; Relative dielectric constant for the medium and the reaction field > epsilon_r = 1 > epsilon_rf = 80 > ; Method for doing Van der Waals > vdw-type = User > ; cut-off lengths > rvdw-switch = 0 > rvdw = 1.4 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = EnerPres > ; Extension of the potential lookup tables beyond the cut-off > table-extension = 1 > ; Seperate tables between energy group pairs > Set energygrps = PNM WT > energygrp_table = PNM WT WT WT > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; 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 > epsilon_surface = 0 > > ; IMPLICIT SOLVENT ALGORITHM > implicit_solvent = 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 > ; Dielectric coefficient of the implicit solvent > gb_epsilon_solvent = 80 > ; Salt concentration in M for Generalized Born models > gb_saltconc = 0 > ; Scaling factors used in the OBC GB model. Default values are OBC(II) > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA > ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. > sa_surface_tension = 2.092 > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = no > ; Groups to couple separately > tc-grps = System > ; Time constant (ps) and reference temperature (K) > tau_t = 0.2 > ref_t = 330 > ; Pressure coupling > Pcoupl = no > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Scaling of reference coordinates, No, All or COM > refcoord_scaling = No > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen-vel = no > > ; OPTIONS FOR BONDS > constraints = none > cutoff-scheme = Group > ``` > I was having trouble getting PNM as part of the energy group, so I added > set energygrps to it, but it still doesnt seem to be working… > On Friday, August 20, 2021 at 5:33:05 PM UTC-4 Christoph Junghans wrote: > >> On Fri, Aug 20, 2021 at 3:26 PM Satyen Dhamankar <[email protected]> >> wrote: >> > >> > I see that VOTCA is running the following command: >> > gmx_196 grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c >> conf.gro >> > >> > And I am getting the following error: >> > Molecule type PNM contains no atoms >> > >> > This is my topol.top file: >> > >> > [ defaults ] >> > >> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> > >> > 1 1 no 0.0 0.0 >> > >> > [ atomtypes ] >> > >> > ; type mass charge ptype sigma epsilon >> > >> > TB 29.04 0.000 A 0.0000 1.0000 >> > >> > TA 43.00 0.000 A 0.0000 1.0000 >> > >> > TI 43.00 0.000 A 0.0000 1.0000 >> > >> > TW 18.01 0.000 A 0.0000 1.0000 >> > >> > [ moleculetypes ] >> More a question for the gromacs mailing list, but I believe this >> needs two [ moleculetype ] sections instead, see >> >> https://github.com/votca/csg-tutorials/blob/master/urea-water/ibi/topol.top#L11-L23 >> >> Christoph >> > >> > ; Name nrexcel >> > >> > PNM 3 >> > >> > WT 1 >> > >> > [ atoms ] >> > >> > ; nr type resnr residue atom cgnr charge mass typeB chargeB massB >> > >> > 1 TB 1 PNM BB 1 0 29.04 >> > >> > 2 TA 1 PNM BA 1 0 43.00 >> > >> > 3 TI 1 PNM BI 1 0 43.00 >> > >> > 4 TW 1 WT BW 1 0 18.01 >> > >> > [ bonds ] >> > >> > ;ai aj funct c0 c1 c2 c3 >> > >> > 1 2 8 1 1.0 >> > >> > 2 3 8 1 1.0 >> > >> > [ angles ] >> > >> > ;ai aj ak funct c0 c1 c2 >> > >> > 1 2 3 8 1 1.0 >> > >> > [ molecules ] >> > >> > ; >> > >> > PNM 1 >> > >> > WT 4046 >> > >> > I don’t understand what is causing this error. I have written similar >> types of topol.top files, and it seems to be working just fine. >> > >> > For completeness sake, this is my conf.gro file: >> > >> > >> > what a nice title >> > >> > 4049 >> > >> > 1PNM BB 1 2.229 1.514 4.238 >> > >> > 1PNM BA 2 2.272 1.286 4.235 >> > >> > 1PNM BI 3 2.194 1.048 4.125 >> > >> > 2WT BW 4 2.276 1.580 1.676 >> > >> > 3WT BW 5 0.119 0.703 0.277 >> > >> > 4WT BW 6 1.682 0.128 4.229 >> > >> > 5WT BW 7 4.889 2.252 2.343 >> > >> > . >> > >> > . >> > >> > . >> > >> > 4045WT BW 4047 1.332 2.041 1.148 >> > >> > 4046WT BW 4048 0.125 1.348 4.089 >> > >> > 4047WT BW 4049 0.839 1.673 3.898 >> > >> > 4.98674 4.98674 4.98674 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 >> > >> > I would appreciate any advice you have for me! >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google >> Groups "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/e6cc499c-35e8-454d-bd08-23c28861cd01n%40googlegroups.com. >> >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/7c13568f-5698-4956-a6f0-d3199e5b63e9n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/7c13568f-5698-4956-a6f0-d3199e5b63e9n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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