[gmx-users] [gmx-developers] how to deal with improper dihedral angles
jalemkul at vt.edu
Mon Feb 29 13:52:45 CET 2016
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
> 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 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
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