On 8/29/13 6:23 PM, Gianluca Interlandi wrote:
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.
Yes, this is typical for comparing energies between software packages.
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).
They did, later in the protein simulations. It seems that they achieved the
expected behavior, though probably other demonstrations could still be done.
In any case, it would be very easy to draw up a simple system of some "standard"
compound in water and calculate energies using both Gromacs and CHARMM using the
"equivalent" (switch/shift differences aside) setups.
-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
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Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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