[gmx-users] bonded interactions in Gromos96

Justin Lemkul jalemkul at vt.edu
Fri Oct 11 18:44:33 CEST 2013



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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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