On 3/6/13 7:35 AM, gromacs query wrote:
Dear All,
How md engine in GROMACS (mdrun) detects which energy function to be used
as it varies for different force fields (FF). Does it detects automatically
from top file format, please correct me if wrong, or some other flag is to
be provided in mdp file? e.g. CHARMM FF function and AMBER FF function has
different way of handling as CHARMM FF includes Urey-Bradley term extra.
All of that information is in the topology at the force field level, which is
all packaged into the .tpr file by grompp. The use of different function types
(e.g. type 5 angles for U-B) covers most of those issues. Other declarations in
top-level force field files handle the rest (combination rules, etc).
-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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