[gmx-developers] how to deal with improper dihedral angles

[Justin Lemkul]

On 2/29/16 3:29 AM, Javaria ashraf wrote:
> hello and good day sir
> i have query related to improper dihedral angles
> my topol.top file shows 1082  improper dihedral angles,
> I have used opls-forcefield, and no water model
> sample:
> 1801  1806  1802  1803     1    improper_Z_CA_X_Y
>   1801  1808  1804  1805     1    improper_Z_CA_X_Y
>   1802  1810  1806  1807     1    improper_Z_CA_X_Y
>   1804  1810  1808  1809     1    improper_Z_CA_X_Y
>   1806  1808  1810  1811     1    improper_Z_CA_X_Y
> .....
> what should i do with them?
> or they will be corrected in energy minimization step?

This is a user connection and is not related to development.  I am CC'ing this 
over to gmx-users.  Please continue with any further questions there.

OPLS uses cpp macros to determine some parameters.  You will find them in 
#define statements in ffbonded.itp.  grompp reads these and applies the 
parameters.  You do not need to take any action.

-Justin

-- 
==================================================

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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