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)?
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
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