[gmx-users] Custom Force Field

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 5 20:22:57 CEST 2009

Honman Yau wrote:
> Dear All,
> Hello! I spent the last couple of hours reading the GROMACS manual and 
> trying to get my head around the files.  One of the things that I want 
> to do is to use a custom force field for ionic liquids related 
> simulations but I don't seem to be able to find instructions on how to 
> do that (probably very trivial...), is there a way to incorporate that 
> into the pdb2gmx interactive force field selection or can you actually 
> specify the force field that you want to use in the command line? Any 
> help would be much appreciated and thank you very much in advance!

If you want to use pdb2gmx, you will need to create all the standard files 
(.rtp, .hdb, nb.itp, bon.itp, etc), create an entry in FF.dat, and increment the 
counter at the top of FF.dat.

Otherwise, it is relatively simple to write your own topology for a limited 
number of species as .itp files.  See Chapter 5 of the manual for the format and 
requirements of all of these files.


> Kind regards,
> Honman
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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