Hi,
On May 24, 2007, at 10:06 AM, [EMAIL PROTECTED] wrote:
My amber experience is probably not good for gromacs since the
logic of using
files is sometimes different (and it seems heating, equilibration and
production is not used often in gromacs, probably due to the fact
you can
isolate thermal bath for different parts of the system).
There's nothing wrong with heating, but in our opinion it's a bit
difficult to control, particularly if you have e.g. lipids and
proteins overlapping in membrane systems that can take multiple
nanoseconds to relax.
Instead, we prefer to use position restraints (typically 1000kJ/mol/
nm, but that's variable) to the heavy atoms during equilibration. The
advantage of position restraints is that even if water/ions/
sidechains initially make bad steric contacts and distort the local
conformation they will gradually be brought back to the reference
positions, and you can monitor the extent of the distortion by
looking at the position restraint term in the energy file.
Cheers,
Erik
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