[gmx-users] Relaxation of protein molecules

[xieyh at hkusua.hku.hk]

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?

Thanks in advance.



Xie YH
Hong Kong Univ.