[gmx-users] Fwd: LJ cut-offs

[Justin Lemkul]

On 1/11/17 1:57 PM, Mohsen Ramezanpour wrote:
> Thanks Justin,
>
> Good to know. I used version 5.0 as Lee et al. 2015.
>
> I agree with you in general about keeping cut-offs the same.
>
> My systems are pure PS lipid membranes.
>
> The study by Klauda in 2016 shows that the higher order in PS membranes
> might be because of PS-PS or PS-K+ interactions.
> However, this was not done in Gromacs.
> This order was intensified when I used Gromacs (version 5.0, though). I
> will do with 5.1.* to see how it improves (hope it works).
>
>
> If PS-PS and PS-K+ interactions are not well defined, which results in
> higher order parameters, what would be a good solution for it?
> 1) reparameterization of PS lipids

Not likely, because what you're observing may be some specific issue related to 
pairwise interactions, which leads to...

> 2) reparameterization of PS-cationic ions interactions

More likely.  NBFIX is applied for some Na+ interactions with lipids, as an 
overly strong interaction was found in some instances.

Depending on how different the results are between what you're doing vs. what 
Klauda published, before investing huge amounts of time into laborious force 
field tuning, contact the Klauda group to see if they can shed any light, or if 
they've observed anything aberrant that they might be actively working on.

> 3) possibly changing the cut-offs, say, 8-10 A.
>

This throws everything out of balance, especially the hydrophobic core, which 
has nothing to do with what you're observing regarding ions.  It's one thing to 
debate an 0.8/1.2 vs. 1.0/1.2 switching distance.  It's a whole other to change 
the cutoff entirely; you break the model by doing this.

-Justin

-- 
==================================================

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

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