rams rams wrote:
Dear Gromacs Users,
I have a problem in running the energy minimization of a protein along
with a substrate. In the .mdp file, if I use constraints = all-bonds,
the system complains like the convergence is reached to system accuracy
not to the one I mentioned.
I don't understand what you mean. It's usually best to copy and paste an
appropriate small amount of actual input and/or output, rather than
filter it through two people's understanding of GROMACS and English. :-)
If I replace the constraints = none, its
running well. I would like to know how serious it is to replace
all-bonds constraints with none.
If your system has bond lengths that already resemble the equilibrium
ones, and the system is not really large, and you're just preparing a
structure for MD, then for EM it really doesn't matter whether you use
constraints.
Mark
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