[gmx-users] Box Exploding Error
Mark.Abraham at anu.edu.au
Sun Jan 11 11:00:37 CET 2009
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
> 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,
> 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.
> 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
Yes, but it has a less flexible form for the potential.
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