[gmx-users] settingparameters for energy minimization

[vivek sharma]

Hi There,
I am trying to do energy minimization of some protein molecule, and I have
following queries for the same.
1. Can I define some RMSD tolerance, such that RMSD value of the molecule
during the energy minimization will not vary more than some predefined
value.
2. Which integrator is better to use SD or CG ?
3. what algorithm should be used for  long-range electrostatic interaction
PME or cut-off.

Please suggest for the above queries.

With thanks,
Vivek
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