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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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