VENKATESH HARIHARAN wrote:
I would like to thank everyone for their help. Several individuals responded
to my initial post.
The consensus seemed to be to use distance restraints.
My question is, because distance restraints
creates penalties if the
distance between two atoms EXCEEDS UPPER BOUNDS, wouldn't that apply more for
pulling
two terminal atoms apart?
So the penalties start really high and get smaller. Where's the problem?
In example, as the peptide is being pulled
apart, if the distance exceeded a certain
value, a penalty would be assessed
to the force. In my simulation, with the terminal ends coming together,
how
UPPER bounds be set? Would I set my upper bounds very low (i.e. - 0.5
nm range)? This way, even the starting
structure, with the distance between
the terminal ends starting at ~3.5 nm, would be assessed a penalty.
Sure, that's the purpose - you're just doing a rough change to suit your
whim, once you're happy with your termini, take off the distance
restraints, equilibrate and simulate for your real objective.
Another
idea suggested by the GROMACS manual was to incorporate a [bonds]
type 6 exclusion in the topology, to create a
harmonic potential between the
two atoms. Would this serve to help bring the two ends together during
simulation?
Yes, but it has a less flexible form for the potential.
Mark
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