[gmx-users] Comb. Rule 2 LJ Params. Being Stored in .tpr as Rule 1 and Vice Versa?
jalemkul at vt.edu
Fri Feb 13 22:42:49 CET 2015
On 2/13/15 2:15 PM, Barnett, James W wrote:
> I have combination rule set as 2 in my [ defaults ] section. However, when I do gmx grompp and then gmx dump on the .tpr file, the values indicate they are being stored as combination 1. My understanding from the manual section 5.3.2 is that for combination rule 2 the last two values on an [ atomtypes ] line are sigma and epsilon. But, the values stored in the .tpr file are c6 (4*eps*sig^6) and c12 (4*eps*sig^12) according to gmx dump.
> Here is an example line from my topology and the corresponding line from gmx dump for both comb. rule 2 and 1:
> [ atomtypes ]
> ; name bond_type mass charge ptype sigma epsilon
> CH3_C CH3 15.03500 0.000 A 3.75000e-01 8.14817e-01; [CH3]-CHX
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 CH3_C 1 NPA C1 1 0 15.035 ; qtot 0
> Combination rule 2 yields in the .tpr file (should be epsilon and sigma, but are actually c6 and c12):
> functype=LJ_SR, c6= 9.06374492e-03, c12= 2.52054979e-05
> Combination rule 1 yields in the .tpr file (should be c6 and c12, but are actually epsilon and sigma):
> functype=LJ_SR, c6= 3.75000000e-01, c12= 8.14817011e-01
By using combination rule 1, you're telling grompp to use what it finds directly
as c6 and c12.
> I am just concerned that this is behavior is opposite of what I expected. Perhaps I am misunderstanding how GROMACS stores these values in the tpr file or the section in the manual? Can someone point me in the right direction?
It's just for storage in the .tpr and how the data are fed into the nonbonded
routines. Internally, everything is done in terms of c6 and c12.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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