[gmx-users] Gromacs Tutorial by Justin
jalemkul at vt.edu
Sat Mar 10 20:56:55 CET 2018
On 3/10/18 1:24 PM, Faezeh Pousaneh wrote:
> Dear Justin
> One more question please,
> Do we need to have constraint in this model of CO2? Isn't it so that we
> have fixed the bond lengths and angles (180) in the topology by this method?
The molecule behaves as a rigid rotor. The math is all laid out in the
tutorial. Since the construction of the O virtual site positions depend
on the bond length connecting the two mass centers (expressed as a
fraction), this (1) makes the math easier, (2) aligns well with known
and easily demonstrated physics, and (3) prevents the need for
parametrizing the bond connecting the two mass centers.
> I run 2 simulations, one with constraints = all-angles and the other
> with constraints
> = all-bonds, I get different results from them. Why?
Please define "different results."
Every simulation will produce different results; no two trajectories
will be binary identical, but their properties should agree within
error. I see no reason why there should be any difference here. There
are no angles to be constrained, nor are there any bonds to be converted
to constraints. There is one explicit constraint in the topology. So
that keyword should be having no effect whatsoever.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users