[gmx-users] Long range Lennard Jones

[Gianluca Interlandi]

And interestingly, they point out at differences between the various 
implementations of the switching function. Also, when trying to replicate 
the CHARMM energies, the authors did not use any cutoff at all and 
performed the calculations in vacuo. If you look at Table 1 in the paper, 
it is exactly LJ where the most discrepancies are, i.e., 0.008 kJ/Mol for 
homeopeptides consisting of 4 AA. I copy the text here (lower left 
corner of page 3, first paragraph of Results):

   For testing the correctness of the force field implementation, we
   compared the values for the potential energy of all amino acids to the
   force field included in the c33b1 release of CHARMM and NAMD version
   2.7b2 (Table 1). The CMAP implementation was also validated by comparing
   forces. These calculations were performed in vacuo without cutoffs,
   since implementation detail differences between CHARMM and GROMACS make
   it difficult to get exactly identical results with other setup schemes.
   For example, CHARMM does not necessarily work with charge groups,
   switch/shift functions are not the same, and deinitions of interaction
   cutoffs differ as well as rules for neighbor searching.

It would have been interesting if they had done the comparions using the 
recommended 10/12/14 cutoff (although PME would have been compulsory 
since gromacs Shift function completely differs from CHARMM SHIFT).

Gianluca

On Thu, 29 Aug 2013, Justin Lemkul wrote:

>
>
> On 8/29/13 5:33 PM, Gianluca Interlandi wrote:
>> And also, gromacs does not seem to use the same switching function as 
>> CHARMM.
>> Has it been tested how much this affects replication of the original CHARMM 
>> MM
>> energies?
>> 
>
> Yes.
>
> dx.doi.org/10.1021/ct900549r
>
> -Justin
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-----------------------------------------------------
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
-----------------------------------------------------