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
>
>
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--
Christoph Junghans
Web: http://www.compphys.de
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