Le 18/04/2023 à 08:21, Steinbrecher, Thomas via AMBER a écrit :
> 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.
Dear all,
First, thanks a lot Thomas for your answer, and sorry for the delay
(paper helpful btw).
Second, in the AMBER 22 manual it is quoted (page 51, pointing to the
reference you mention):
""""
A word of caution regarding barostat and cut off selection with lipid
simulations. It is well known that lipids
can be very sensitive to simulation conditions. Previous advice has been
to use the Berendsen barostat and a 10A
cutoff when simulating lipids with the AMBER Lipid force fields. This
was due to bilayer deformation that was
regularly seen with simulations run using the Monte Carlo Barostat.
Recent work by Gomez et al.[90] investigated
this behavior and determined that there are issues when using the MC
barostat with hard Lennard-Jones cutoffs.
The issue affects all simulations but is most obvious when simulating
lipid bilayers. Gomez et al recommend use
of an LJ force switch when running simulations with the MC barostat.
""""
So the 10.0 cutoff was only for avoiding membrane deformation (buckling
or thickening), but this was not in fact
the problem at all (I'm not using MC). Good to see there is a clear
explanation.
In the meantime I have done several MD (article in progress) to ensure
these settings (8 versus 10) had no impact
on my system of interest, at least on the motions I am interested in.
Thanks again for the answer, I found only recently this information
while showing the manual to students, always RTFM!
Best,
Stéphane
--
Maître de conférences Hors Classe, PEDR, HDR
US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics, F-44000 Nantes
http://www.us2b.univ-nantes.fr/ -http://www.steletch.org
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 11 2024 - 11:30:03 PDT
