[gmx-users] cut-off

[Faezeh Pousaneh]

Thanks Justin.

yes, you are right, my simulation is very sensitive to cut-off.

I did not understand what do you meant by '' is the balance of forces
correct''?

So If I understood you correctly, the cut-off lengths must be chosen from
the force filed, yes?
Since I am not expert how to choose a force field, could you tell me a
proper force field for Benzene all-atom model?

Best regards


On Thu, Jun 18, 2015 at 1:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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