[gmx-users] adding new parameters to force field
mark.j.abraham at gmail.com
Thu Dec 22 07:07:04 CET 2016
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 still
> 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 that
> (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 of
> 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 force
> field files, be-
> cause all non-bonded parameters above the last [ atomtypes ] section would
> be overwritten
> using the standard combination rules.
> *Rewards work better than punishment ...*
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