[gmx-users] Verlet AND tabulated potential
tkarpati at gmail.com
Tue Jul 8 11:36:00 CEST 2014
Thank you for your quick answer. I understand now that I should not temper
with Buckingham potentials (and/or tables) along with Verlet cut-offs.
Performance is not an issue at this stage but I wonder whether definition
of charge groups can be useful for a crystal at all. As far as I can see
unit cells of bulk isotropic materials could be grouped so -until any
chemical change of the matrix (or surface) takes place which perturbes it.
Thus, two question remains: (i) can I sensefully define charge groups
for a crystal and (ii) can I do it without running out of the 32 groups limit?
Once again, thank you very much -your answer saved me valuable time.
On Tue, Jul 8, 2014 at 9:50 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> On Mon, Jul 7, 2014 at 3:17 PM, Tamas Karpati <tkarpati at gmail.com> wrote:
>> Dear all,
>> I have trouble creating a FF without bonds explicitely defined,
>> only using "nonbonding" forces of the Buckingham (BH) type to keep
>> my crystal in one piece. The problem is related to wrong interatomic
>> forces on basis of the ASCII-dumped TRR files. So FF works (at
>> least functionally), optimization does not.
>> Since replacement of BH by an approximate LJ potential succeeded
>> I decided to by-pass the built-in BH code by a tabulated potential.
>> Unfortunately, GROMACS (versions 4.6.3, 4.6.5, 5.0-beta2 and 5.0)
>> wouldn't take my MDP file.
>> I kindly ask your help on the subject. The typical error message
>> is coming from GROMPP in the forms:
>> 1. "With Verlet lists only cut-off and PME LJ interactions are supported"
>> 2. "With Verlet lists only cut-off, reaction-field, PME and Ewald
>> electrostatics are supported"
>> Never mind the LJ statement above as the same appears with BH, as well.
>> The forcefield.itp/[default] contains nbfunc=2 and comb-rule=1.
>> The connected part of the MDP file is
>> cutoff-scheme = verlet
>> vdwtype = User
>> coulombtype = User
>> I seem to be incompatible (in fact new to) GROMACS or User does not
>> much like Verlet cut-offs. I'm stuck. If you have any idea or working
>> example, please share it. I'v failed locating relevant info on the Internet
>> so far.
> As the errors suggest, Buckingham interactions are not supported with the
> Verlet cut-off scheme (and neither are user tables, yet). The group cut-off
> scheme has support for Buckingham interactions, but only in the plain-C
> non-SIMD kernels, which are not fast. You can probably do better (ie. get
> SIMD) by using a user table there.
> Thanks in advance,
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