[gmx-users] cut-off

[Faezeh Pousaneh]

thanks David.
but I am wondering for example if a chosen short cut-off produces correct
experimental data, should I still make it larger or PME?

No that is an all-atom model.


Best regards


On Wed, Jun 17, 2015 at 2:50 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 17/06/15 14:22, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> Does the choice of cut-off length depends on the chosen force filed? or it
>> can be chosen such that the simulation produces the experimental values?
>>
> Cutoff should be used consistently, each force field has their setting,
> however that does not mean these settings are optimal.
> Here is a recent paper on organic liquids discussing this.
> http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00190
>
>
>
>> In my case, I simulation Benzene with Gromos54A7 and I choose 1.2 nm for
>> both LJ and coul interactions, is that fine?
>>
> Is it united atom? In that case you have no Coulomb. However from our work
> above it follows that 1.2 nm is too short and for accurate results you need
> to use PME for both Coulomb and Van der Waals.
>
>>
>> thanks
>> Best regards
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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