[gmx-users] Why density increase with increasing the cutoff length?
David van der Spoel
spoel at xray.bmc.uu.se
Mon Dec 21 09:01:57 CET 2009
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
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.
> 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 University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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