[gmx-users] Long range Lennard Jones

Gianluca Interlandi gianluca at u.washington.edu
Thu Aug 29 20:52:53 CEST 2013

> That's good to know that you've tested different setups.  Are the water 
> interaction energies comparable?  Have you tested model compounds or just 
> full proteins?  Over how long of a time period?

I have tested only full proteins over a 50-ns period. I have not 
calculated yet the water interaction energies. Do you mean by that just 
the force field interaction energy bulk-bulk? I plan to test how much it 
affects FEP calculations.

>> Finally, I have not tested it in gromacs, but in NAMD there is a 
>> performance gain of 25% when using the shorter cutoff. This is a factor 
>> to consider. When I asked for Teragrid supercomputing allocations back 
>> in 2006 and 2007 and I suggested 10/12/14 cutoff, the reviewers always 
>> complained and cut my requested time of 20% with the justification that 
>> I must use a shorter cutoff.

> That's unfortunate.  In my opinion, it is shameful that desired 
> performance exceeds proven integrity of the data.

I mean, performance is a factor to consider when accuracy is not affected. 
I don't recall what the reviewer's reasoning was. They probably did their 
recommendation in good faith that it won't affect accuracy. But I agree 
that one should test how much the system is affected.


Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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