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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