[gmx-users] problem with gromacs 3.0

[Anton Feenstra]

prakash sista wrote:
> 
> Hi,
> I am working on YKGQP peptide sequence. My friend has done a few
> simulations on the same peptide with some mdp parameters on
> gromacs 2.0. Now when I try to use the same parameters as he used
> on gromacs 3.0, I get the following error. I am not able to
> understand why this error is surfacing when there is no such error
> in gromacs 2.0.
> 
> ERROR: rcoulomb must be >= rlist
> ERROR: rvdw must be >= rlist

The definitions of some of the .mdp parameters has been made more
consistent. I don't remember how it was exactly in 2.0, but in 3.x
it is like this: rlist sets the shell of particles for which all
interactions will be calculated at each timestep (i.e. the 'short'
cut-off). rcoulomb/rvdw set the shell of particles for which any
interactions will be calculated at each 'nstlist' timestep (i.e.
the 'long' cut-off). It doesn't make sense therefore to have them
shorter than rlist, since then you will include particles in your
neighborlist (inner shell) for which you are not going to calculate
interactions.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
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|  \__/  | "Engage" (J.L. Picard)                                    |
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