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
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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