Grace Li wrote:
Hello,
I am having some trouble using distance restraints. My goal is to apply a
harmonic potential to the distance between two atoms in a short peptide
(35 residues). Doing simulations in vacuo, both of the following
techniques worked to restrain the distance. Also, both techniques worked
for simulations in water without periodic boundary conditions. As soon
as I include pbc = xyz in my .mdp file and use PME for the electrostatics,
my simulation crashes (producing step0.pdb and step-1.pdb). I am assuming
this is because GROMACS is using the distance to the image of the other
atom, not the actual distance in the box? Is there any way of getting
around PBC for distance restraints?
Before you assume the distance restraints are the problem, you should
try the simulation in water and/or vacuum PBC without this interaction.
Mark
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