[gmx-users] inversion potential
nimavaeesa at yahoo.com
Thu Aug 20 16:43:46 CEST 2015
Hi, Dear gromacs usersI want to define some bond parameters within opls-aa force field, which are taken from a paper. I know how to define nonbonded parameters as well as bonds and angles and dihedrals. But I don't know how to define a so-called inversion potential and the paper is vague on this. The paper reads:
u_inversion(theta_ijk-theta_0)=K1(theta_ijk-theta_0)+K2(theta_ijk-theta_0)^2inversion theta0(deg) K1(kcal/mol/rad) K2(kcal/mol/rad^2) C1 360 -60 30
The only way to define such a form of potential in gromacs, as I found out from the manual, is to use a quartic angle (please see table 5.5 of the manual). The manual says that one has to specify 3 atoms to define such an angle potential. However, the paper has specified only one atom (C1)!! Although it has not clarified, it seems that the paper is using this potential to avoid the rotation of the mentioned atom (due to theta0=360 deg).
Does anyone happen to know the answers to the following questions:1- What is this inversion potential used for?2-How can I implement it in Gromacs?I appreciate any kind comments on this issue.Thanks.Nima Azar
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