On 6/11/13 4:12 PM, Steven Neumann wrote:
Dear Gromacs Users,
I got really confused: In manual [defualts ]:
"nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
(Buckingham)"
I want to use mdrun -table table.xvg with my own potential, which one I
should choose?
"gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4
parameters from the pairtypes list. When parameters are not present in the
list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that
are not present in the pair list from normal Lennard-Jones parameters using
fudgeLJ"
I want to have all intramolecular atoms (within my chain) interacting (no
exclusions) with each other from [ atomtypes ] in ffnonbonded.itp
Does it mean "yes" with nrexcl =1 in my topology?
And sth I also got confused:
[ pairtypes ] are only 1-4 parameters or here I can specify parameters for
all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also
correspond to intra molecular interactions?
These topics are discussed frequently. Please search the archive; surely you
will find relevant topics.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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