[gmx-users] md engine detection for different force field

[Justin Lemkul]

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

-- 
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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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