Hi Marc,
With "cutoff-scheme = Group" gromacs should not give the same error again. Did you clear the 'step_*' directories from the previous run and reran? It may be the case than you only updated grompp.mdp in the main directory and forgot to update the grompp.mdp in the step_001. Please check if that the case. If not please post the last few lines from inverse.log which describe above error. Thanks, Sikandar On Fri, Sep 18, 2015 at 10:34 AM, Marc Charendoff <[email protected]> wrote: > Hello, > > I tried the "cutoff-scheme = Group" insertion into the mdp file but it did > not work. I got the very same errors as originally stated. Thoughts? > > Thanks, Marc > > ------------------------------ > *From:* Christoph Junghans <[email protected]> > *To:* "[email protected]" <[email protected]> > *Sent:* Thursday, September 17, 2015 5:04 PM > *Subject:* Re: [votca] Water csg_inverse tutorial > > 2015-09-17 13:37 GMT-06:00 Marc Charendoff <[email protected]>: > > Moved on beyond the last posed question - figured out which options to > > clear. Now attempting to run csg_inverse per the water tutorial (using > > lastest VOTCA and Gromacs 5.0.2): > > > > ERROR 1 [file grompp.mdp]: > > With Verlet lists only cut-off and PME LJ interactions are supported > > > > ERROR 2 [file grompp.mdp]: > > With Verlet lists only cut-off, reaction-field, PME and Ewald > > electrostatics are supported > > > > grompp.mdp file in the ibi directory of the tutorial for lists, > > Electrostatics and VDW are as follows (I know there is a deprecation of > > group-based cut-offs in 5.0, but per the error it looks like Verlet is > > being invoked which I'm not so sure it is) Is this a grompp.mdp error or > > something with Votca? > Yes. this is a gromacs problem! Even though group-based kernel have > been deprecated, gromacs 5.0/5.1 does not support tabulated > interactions, which are needed for VOTCA, in the new verlet cutoff > scheme. > > As a workaround just add "cutoff-scheme = Group" to the mdp file. > In votca-1.3-dev we do that trick automatically. The tutorial assumes > that you have the dev version install, that is what the "d" in > "./build.sh --prefix ${prefix} -ud ..." in Installation section stands > for. > > Christoph > > > > > > > ; NEIGHBORSEARCHING PARAMETERS > > ; nblist update frequency > > nstlist = 10 > > ; ns algorithm (simple or grid) > > ns-type = Grid > > ; Periodic boundary conditions: xyz, no, xy > > pbc = xyz > > periodic_molecules = no > > ; nblist cut-off > > rlist = 1 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = User > > rcoulomb-switch = 0 > > rcoulomb = 0.9 > > ; 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 = 0.9 > > ; 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 > > energygrp_table = CG CG > > ; 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 > > optimize_fft = no > > > > > > > -- > > 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 post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > > > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
