On 10/11/13 12:40 PM, Ehsan Sadeghi wrote:
Hi gromacs users,
I tried to add new bonded interactions to the ffbonded.itp file in gromos96,
but I am confused about the used parameters in the descriptions. Here is an
example:
#define gb_1 0.1000 1.5700e+07
; H - OA 750
The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2
I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition:
0.1000, 1.5700e+07, 750.
The same story for the angle potential:
#define ga_1 90.00 380.00
; NR(heme) - FE - C 90
The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) -
cos(theta0_ijk))^2
I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the
definition: 90.00, 380, 90.
The numbers in the comment lines are bond indices from the Gromos96 force field
files. They are irrelevant.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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