[gmx-users] adding new parameters to force field
ramezanpour.mohsen at gmail.com
Thu Dec 22 00:07:43 CET 2016
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
using the standard combination rules.
*Rewards work better than punishment ...*
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