[gmx-users] question about preferred values in itp files

Justin Lemkul jalemkul at vt.edu
Thu Apr 14 13:45:52 CEST 2016

On 4/14/16 6:41 AM, abhishek khetan wrote:
> Dear Justin ans Tsjerk,
> Thanks for your replies. I think I asked Q3 in a stupid way, its totally
> not what you think it is. A better way to ask would be as follows:
> Lets say I have box of 216 acetonitrile (CH3CN) solvent molecules, the
> initial geometry file (lets say acn216.gro) for which I generated using the
> insert-molecules routine from gromacs by passing the geometry of a single
> CH3CN molecule (lets say acn.pdb), which was optimized at very high level
> of quantum chemistry theory. In the acn.pdb the C-N bond length is 0.1145
> nm. Lets say I want this length to be the equilibrium length in a single
> molecule. and the harmonic potential acts when the bond length devaites
> from this value. The acn216.gro file has position data for all molecules
> such that bondlengths and angles are exactly at the equilibrium values
> within every molecule (before I do any energy minimization or nvt/npt).
> However, lets consider the equiliibrium C-N bond between opls_754(CZ) and
> opls_753(NZ) obtained from the ffbonded.itp. To find out the equilibrium
> bond distance between these two what I do is:
> $ grep  "CZ    NZ" oplsaa.ff/ffbonded.itp
> Which gives me:
>    CZ    NZ      1    0.11570   543920.0   ; wlj 9/98
> This gives the equilibrium bond length as 0.11570 nm. May be the difference
> is too small to have any perceptible change. But the real question is if
> this value from ffbonded.itp is taken as the default equilibrium bondlength
> value or does my specified value of 0.1145 take preference as the new
> equilibrium bond length, just like it does for the atomic charges and
> masses.
> TL;DR - If I want to specify new equilibrium bond length values, then do I
> have to create new atom types with new force constants that decide the
> harmonic potential or does gromacs use the new equilibrium bond lengths
> from the input geometry with the force constants specified in the
> ffbonded.itp file?

Whatever you specify in your topology is definitive.  You can override the 
values in ffbonded.itp with whatever you want in the molecule's topology.

Beware though, that if you start changing bond lengths, you're imbalancing 
elements in the force field...not a good idea.



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


More information about the gromacs.org_gmx-users mailing list