[gmx-users] Relaxation of protein molecules
feenstra at few.vu.nl
Mon Jan 3 18:23:39 CET 2005
xieyh at hkusua.hku.hk wrote:
> Dear GMX users:
> I am trying to simulate one protein fragment in water with the applied electric
> field. In my case, the protein pdb file is not downloaded from PDB database,
> instead, I use other software to generate it.
> Normally, we perform the simulation as the following processes: EM (in water)
> --> PR (in water) --> md. However, the pdb structure generated from other
> software is much more idea and regular, without the necessary relaxation.
> So, before my md simulation with the applied electric field, I also make an
> additional relaxation progress in water (the electric field is not considered
> in this step). But, during this relaxation, the protein chain becomes quite
> irregular. That's not what I need.
> Because this relaxation is also very important for my simulation, anybody can
> tell me how I should perform this relaxation? That should followe which step?
You could also turn on PR during EM, and I normally include an EM step
without water as well, because the water prevents mdrun from rigorously
minimizing your protein. (Perhaps you could use a 'freezegroup' to exclude
the water from minimization, haven't tried that.)
So you could:
1) strip off the water
2) EM + PR on the protein
3) add back the stripped water (assuming the protein didn't change too much.)
4) keep PR on the protein, and perform EM on (protein +) water
5) keep PR on the protein, and perform MD (1-10 ps) on (protein +) water
Additionally, you may want to release the sidechains of the protein first,
so they can relax before you let the backbone free as well:
6) PR on protein backbome, MD (10-100ps) on protein + water.
7) 'free' MD
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