[gmx-users] cut-off

[Justin Lemkul]

On 6/18/15 7:25 AM, Faezeh Pousaneh wrote:
> 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?
>

Playing with cutoffs to try to force models to behave a certain way.  You might 
get a "right" answer, but is the balance of forces correct?  Force fields are 
generally tuned to be used with specific nonbonded regimes and shouldn't be 
altered unless systematic studies of those setups have been done.

> No that is an all-atom model.
>

Just for pedantic sake, GROMOS96 54A7 is indeed a UA force field, but aromatic H 
are represented explicitly.  So in this case, the electrostatic treatment is 
indeed important.  PME makes the Coulombic cutoff a bit more flexible, but van 
der Waals interactions are going to be significant in a system like this and can 
be very sensitive to changes in the cutoff.

-Justin

>
> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================