[gmx-users] Why density increase with increasing the cutoff length?
x.periole at rug.nl
Mon Dec 21 09:18:39 CET 2009
On Dec 21, 2009, at 9:01 AM, David van der Spoel wrote:
> On 12/21/09 8:55 AM, XAvier Periole wrote:
>> Would it be all cut-offs: elect + vdW ? Or the increase is separate?
>> For your info the vdW are attractive potentials at long distances so
>> an increase of cutoff would result in an increase of attraction and
>> therefore to an increase of density!
>> This is one good illustration of the fact that you should not change
>> the cutoff values from the ones used for the parameterization of a
>> force field.
> In general I agree, however for some popular force fields like OPLS
> this is not so well-defined. Jorgensen uses different cut-offs in
> different papers.
This is rather a bad example :)) With all due respect to Jorgensen, it
does not mean
this is something to do!
> Using PME and dispersion correction means you are almost independent
> of the cut-off length (if they are not too short). Typically 1 nm
> and upwards will give you the same results with these settings.
> If you're using plain cut-offs
> or RF you're on your own.
Then the cutoffs are defined so no problem :))
But I think we all agree on these issues: the treatment of long-range
are delicate :))
>> On Dec 21, 2009, at 8:03 AM, Yanmei Song wrote:
>>> Dear Users:
>>> Anyone can explain why the density of the water models increase with
>>> increase the cutoff length. I tried a couple water models in
>>> reaction-field, PME simulations.The cutoff length ranged from 0.9 to
>>> 1.5. They all show the same trend. Then there must be some reasons.
>>> Anyone can tell me why?
>>> Yanmei Song
>>> Ph.D. Candidate
>>> Department of Chemical Engineering
>>> Arizona State University
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> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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