[gmx-users] bonded interactions in Gromos96

Ehsan Sadeghi esa38 at sfu.ca
Fri Oct 11 19:31:14 CEST 2013

Thanks Justin.

Do you know how can I find these coefficients for the atom interactions which are not defined in Gromos? I have (-(CF2CF2)4 -)(-O-CF2CF(CF3 )-O-CF2 CF2-SO3H) molecule. I need C-F, C-S, C-S-O interactions. Can I use predefined ones? which one?

All the best,

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, October 11, 2013 9:44:33 AM
Subject: Re: [gmx-users] bonded interactions in Gromos96

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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