[gmx-users] Units within Packaged OPLS Force Field File (ffbonded.itp)
Matthew.P.Howenstine.1 at nd.edu
Wed Apr 25 23:30:08 CEST 2018
Thank you so much for the assistance, and apologies that the question had
it’s answer within the user manual. I’m ashamed I had missed that when
looking through the manual the past few days. As that guide lays out the
exact units for each, and the fact that the OPLS-AA forcefield .itp files
follows that syntax for the for the func. types, that should be perfect and
mean that all .itp files in the distribution are already in proper units.
Thank you once again -
On Wed, Apr 25, 2018 at 3:08 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> > 5.0.7) are - I have seen various sources on the OPLS units, and have
> > 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
> > file online where a different value was used for the benzene improper
> > dihedral. Essentially, is there any source which outlines exactly the
> > within ffbonded.itp, or do you just have to back-reference the GROMACS
> > manual's functional forms as they have already been converted to the
> > 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 A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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