[gmx-users] Long range Lennard Jones

[Gianluca Interlandi]

Yes, I've seen that thread before. My feeling is that simulating membranes 
with the CHARMM36 FF is a different story. It's good to be aware of that.

Gianluca

On Thu, 29 Aug 2013, Justin Lemkul wrote:

>
>
> On 8/29/13 5:15 PM, Gianluca Interlandi wrote:
>>> Of course, if accuracy is not in question then performance dominates.  I 
>>> have
>>> seen countless reports on this list and elsewhere where small changes in
>>> cutoffs lead to wildly incorrect behavior, affecting every force field. 
>>> Thus,
>>> I am always extremely skeptical of such changes.  The effects can be 
>>> subtle
>>> but non-negligible.
>> 
>> I would be very interested in reading about some of these reports. I have
>> searched the gromacs forum and I have found similar discussions but never
>> accompanied by actual benchmarks with numbers, or maybe I have not searched
>> carefully enough!
>> 
>
> They tend to show up in reports of crashes, structures falling apart, and 
> failure to reproduce membrane properties (which is extremely sensitive to 
> cutoff values).
>
> One such example that I recall having occurred recently:
>
> http://lists.gromacs.org/pipermail/gmx-users/2013-January/078269.html
>
> Previous posts in that thread have lots of information.
>
> -Justin
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
-----------------------------------------------------