[gmx-users] Relaxation of protein molecules

[Anton Feenstra]

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.

And, finally,
7) 'free' MD


-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|