[gmx-users] Question

[Justin Lemkul]

On 1/26/16 2:51 PM, Eric Smoll wrote:
> Hello Gromacs users,
>
> When running pdb2gmx, what determines the function number used for each
> type of potential (bonds, angles, dihedrals, etc.). When I run pdb2gmx, my
> dihedrals section is built with function number 3. I would like to change
> this to function number 5. It is easy to edit the file manually but is
> there a recommended way to do this?
>

The force field itself dictates this.  Change the functional form and (1) you 
change the nature of the force field and (2, more importantly) probably render 
the topology nonfunctional because there won't be matching terms.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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