WU Yanbin wrote:
Hi, all,
According to Manual v3.3, "It's possible to apply multiple bonded
interactions of the same type on the same atoms" [12th line of Page 98].
If a dihedral potential for 4 neighboring atoms is defined 3 times using
the "periodic type" in the topology file, like
V=k1*(1+cos(phi-phi_s1))
V=k2*(1+cos(2*phi-phi_s2))
V=k3*(1+cos(3*phi-phi_s3))
would GROMACS recognize the dihedral potential as the sum of the above
three, or just the 3rd one (which is defined last)?
If GROMACS recognizes the dihedral potential as the sum, then this can
be another way to define OPLS force filed in GROMACS.
Bonded interactions are summed. Surely this is in the manual somewhere, but it
certainly has been discussed in the list archive many times.
I think you might find this discussion relevant:
http://lists.gromacs.org/pipermail/gmx-users/2007-July/028639.html
-Justin
Does anyone know the answer? Thanks.
Best,
Yanbin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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