Yes, I had to take some time understanding GROMACS functionality to get it all working. Thank you for the advice!
On Friday, August 20, 2021 at 7:41:04 PM UTC-4 Christoph Junghans wrote: > > > 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. 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/3ecd01d4-f375-4f58-bba5-4d023c863722n%40googlegroups.com.
