[gmx-users] Why density increase with increasing the cutoff length?

[David van der Spoel]

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.

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
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
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