[gmx-users] adding new parameters to force field
ramezanpour.mohsen at gmail.com
Thu Dec 22 21:06:48 CET 2016
Thanks Mark, :-)
Maybe my question was not clear.
I have a molecule and I am trying to parametrize it.
I have assigned atom types to each atom and now trying to find the
approperiate bonded and nonbonded parameters for it.
Based on these atom types, there are parameters for it in FF already.
However, the parameters (especially, the dihedrals) do not result in
reasonable agreement with exp data.
So, I had to optimize the parameters for a few specific dihedrals (keeping
the same atom types).
Now, I want to add new parameters into the force field. This is why I was
curious to see if grompp will read the new inserted parameters or the
In gromos force field, each bond, angle, dihedral has a code (e.g. gb_1,
ga_1, and gd_1), thus, I can specifically define which one to use for my
However, in Charmm36, there is not any similar code. So, I was not sure
which parameter grompp will uses.
One solution was to add new optimized parameters in corresponding line in
molecule.itp file. (there are a lot of lines and I rather to included lines
in ff than molecule.itp file)
An alternative was to define new atom types with similar properties but new
dihedral parameters compared to original ones.
I checked it yesterday and interestingly, grompp gives warnings regarding
duplicates, which one it takes, and if it overrides original parameters or
On Wed, Dec 21, 2016 at 11:06 PM, Mark Abraham <mark.j.abraham at gmail.com>
> Sometimes. It depends exactly which functions and function types, and
> whether it's part of a moleculetype. If you don't want something, don't
> include it :-)
> On Thu, 22 Dec 2016 10:07 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com
> > Dear Gromacs users,
> > I have a new file with both bonded and nonbonded parameters for some atom
> > types in it. I want to use these new parameters for simulation and ignore
> > the parameters in force field ( if there is any parameter already exist).
> > 1) If I add the lines from each section of new file at the end of
> > corresponding section at ffbonded.itp and ffnonbonded.itp files, do I
> > need to comment out all the present parameters or they will be all
> > overwritten by new defined parameters?
> > 2) How if I just #include new file after inclusion of normal force field?
> > Will it overwrite previous parameters?
> > Reading gromacs forum discussions and manual, I still was not sure of
> > (I am using gromacs versions 4 and 5).
> > *From manual 5.8.3.*
> > *Adding atom types*
> > As of GROMACS version 3.1.3, atom types can be added in an extra [
> > atomtypes ] section
> > after the the inclusion of the normal force field. After the definition
> > the *new atom type(s)*, ad-
> > ditional non-bonded and pair parameters can be defined. In pre-3.1.3
> > versions of GROMACS, the
> > new atom types needed to be added in the [ atomtypes ] section of the
> > field files, be-
> > cause all non-bonded parameters above the last [ atomtypes ] section
> > be overwritten
> > using the standard combination rules.
> > Best,
> > Mohsen
> > --
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