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

abhishek khetan askhetan at gmail.com
Thu Apr 14 12:42:00 CEST 2016

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

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?

I hope I was clear this time. Thanks again.


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