On 9/5/13 12:53 AM, Dallas Warren wrote:
Going through the GROMOS53a6 parameters, found that there appears to be an
inconsistency between what is present within the ffnonbonded.itp file and that
quoted within the paper (Ooostenbrink et al 2004
http://dx.doi.org/10.1002/Jcc.20090) for the c12 LJ values for CH2 and CH3 in
the [ pairtypes ] section.
[ pairtypes ]
; i j func c6 c12
....
OA OA 1 0.0022619536 1.265625e-06
....
CH2 CH2 1 0.0047238129 4.7419261e-06
....
CH3 CH3 1 0.0068525284 6.0308652e-06
Then taking these c12 parameters from the ffnonbonded.itp file and converting
to square root values so can compare with the values presented in the FF paper,
Table 9. Have also done the reverse, converting the Table 9 c12 values to the
squared value so can compare with the value within the ffnonbonded.itp
OA - OA
ffnonbonded.itp 1.265625e-06 => 0.001125000
Table 9 1.265625E-06 <= 0.001125
CH2 - OA
ffnonbonded.itp 4.7419261e-06 => 0.002177596
Table 9 4.743684E-06 <= 0.002178
CH3 - OA
ffnonbonded.itp 6.0308652e-06 => 0.002455782
Table 9 6.031936E-06 <= 0.002456
As you can see, the parameters for OA are consistent, while those for CH2 and
CH3 are not.
So, I suppose the questions are:
1) where did the values presented in the ffnonbonded.itp actually come from?
2) why are they not consistent with those that are defined in the FF paper,
considering that the other cases are i.e. OA?
3) how much of a concern it that the values are that different (4th significant
figure)?
The values in ffnonbonded.itp came from Gromos96 force field files via a script
that did the unit conversion. If you go to the ATB site, you can find the
original 53a6 force field files and you will see that the values in
ffnonbonded.itp are actually correct. There are more significant figures for
some of the terms than are presented in the paper. Both of the values you have
shown above, back-calculated from ffnonbonded.itp, actually reproduce the C12
values in these files exactly.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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