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

[gromacs query]

Thanks a lot Dr. Justin

On Wed, Mar 6, 2013 at 2:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>