[gmx-users] Units within Packaged OPLS Force Field File (ffbonded.itp)

Justin Lemkul jalemkul at vt.edu
Wed Apr 25 21:08:00 CEST 2018



On 4/25/18 2:23 PM, Matthew Howenstine wrote:
> All,
>
> I was just confirming what the units within the
> prepackaged \share\top\oplsaa.ff\ffbonded.itp file (within Gromacs version
> 5.0.7) are - I have seen various sources on the OPLS units, and have mostly
> confirmed that most all are already converted to a kJ basis within this
> file (i.e. harmonic bond angle force constant [kJ/mol/rad^2],
> Ryckaert-Bellemans constants [kJ/mol]). My main question was in the
> improper angle's periodic force constant at the bottom -
>
> i.e. in the lines:
> ; Z -CA-X -Y improper torsion. CA is any ring carbon
> (CA,CB,CN,CV,CW,CR,CK,CQ,CS,C*)
> #define improper_Z_CA_X_Y 180.0 4.60240 2
>
> Is the 4.60240 in kcal/mol or kJ/mol? I found one OPLS derived force field
> file online where a different value was used for the benzene improper
> dihedral. Essentially, is there any source which outlines exactly the units
> within ffbonded.itp, or do you just have to back-reference the GROMACS user
> manual's functional forms as they have already been converted to the proper
> form before inclusion within the Gromacs distribution?

Everything is in Table 5.5 of the manual, which also links to sections 
describing those functional forms.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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