Hi Stephane,
my guess is, it might be related to this article
https://pubmed.ncbi.nlm.nih.gov/34921560/ about lipid density distortions
for some barostats(including the Amber default one) and iirc, the behaviour
described there is more pronounced with a smaller real space cutoff, so
maybe some people have defaulted to more conservative cutoffs for membrane
simulations?
Apart from such specific artefacts, I would estimate/hope that different
cutoffs in a sensible range of say 7-12A should not impact your simulation
behaviour all that much, you are just trading a little 'realism' against
computational efficiency if you make the cutoff smaller.
There could be other reasons I am not aware of, based on FF development or
something else, of course.
Kind Regards,
Thomas
On Mon, Apr 17, 2023 at 6:32 PM Téletchéa Stéphane via AMBER <
amber.ambermd.org> wrote:
> Le 17/04/2023 à 18:29, Téletchéa Stéphane via AMBER a écrit :
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> Dear all, this is the second time I send this question, and the body
> part is pruned...
>
> Original text :
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> I'm a long term user of AMBER but probably missed some important steps
> in FF development,
> since I was used to a 8.0 cutoff for old FF, but I see here and there a
> cutoff of 10.0 being used,
> and sometimes mixed between parameters or articles.
>
> For instance, in tutorial "3.1 Relaxtion of Explicit Water Systems", the
> 1min.in file contains "cut=10.0",
> but the 3md.in file contains "cut=8.0", as indicated as the default
> value in AMBER manual.
>
> I have also seen this cutoff value of 10.0 for the recent lipids21 force
> field publication, and the accompanying
> github files.
>
> Is there a strong bias by using 10 or 8 for protein FF (FFSB14 or FFSB19
> ?) and/or a protein in a lipid membrane?
>
> Thanks a lot for clarification, this is puzzling me, and I have not
> found a simple answer to it.
>
> Stéphane
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> --
> Associate Professor in BioInformatics, US2B, Nantes Université, CNRS, UMR
> 6286, Team Protein Design In Silico
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
> Nantes cedex 03, France
> Tél : +33 251 125 636 / Fax : +33 251 125 632
> http://www.us2b.univ-nantes.fr/ - http://www.steletch.org
>
>
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
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4070 Basel
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Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Mon Apr 17 2023 - 23:30:02 PDT
