[gmx-developers] Morse as non bonded (?)

[David van der Spoel]

Marcelo A. Carignano wrote:
> Than you very much David,
> I will try with the nb_generic code to see it I can make it work.
> 
> But, if you say the tables are more efficient, then I will try again
> with them.
> I have a problem though, the simulation gives a segmentation fault as
> soon as
> two atoms are within the cut-off distance (r < r_cutoff).
> This happens for a system that consists of chain molecules (just 5
> beads, bonded
> with fourth power bonds and harmonic angles, exclusion among the five).
> One chain runs fine, two chains (interacting via table) dont. The
> program crashes.

Could it be a problem with units? Gromacs expects nm and kJ/mol.
Often crashes are due to problems with the physics.

> If instead of the chain molecules I have only point particles
> interacting with the same table,
> everything goes well.
> I could't find a solution by modifying the parameters (temp, tau, dt, etc).
> Do you have any idea where to look for the problem?
> 
> I am using v4.0.4; and try both single and double precision, with the
> respective
> recommended table spacing.
> 
> Thanks again.
> Marcelo.
> --
> David van der Spoel wrote:
>> Marcelo A. Carignano wrote:
>>> Salut,
>>>
>>> Morse potentials are implemented in gromacs as a bond type.
>>> However, the potential has the interesting feature that allows an
>>> independent control
>>> of the depth, core size and range of the interactions (I need something
>>> like that).
>>> Therefore, using Morse potential as non-bonding will be useful for me,
>>> and possible others.
>>>
>>> The question is how difficult would be to modify the code, using as base
>>> the Morse code
>>> for bonds, to write a Morse code for non-bonding. I am willing to
>>> attempt this, if I get some
>>> general indications (I can use also very detailed indications) from
>>> those of you who know
>>> the code with sufficient detail to provide some advise.
>>>
>>> I know that I can use the tables, but that is not the solution I am
>>> looking for.
>> Why not? It is very efficient (much more efficient than analytical
>> code). The bonded Morse code is quite simple (src/gmxlib/bondfree.c).
>> There is also a generic nonbonded kernel (in C) for you to play with
>> in src/gmxlib/nonbonded/nb_generic.c.
>>
>> The real interesting thing in my opinion would be to have non-bonded
>> three-body interactions...
>>
>>> Many thanks,
>>>
>>> Marcelo Carignano
>>> -- 
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>>
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se