[gmx-users] steered md - pushing

[Tamas Hegedus]

Hi,

I have a protein with four domains.
I know the conformation of the full protein in one state.
In the other state I know only the conformation of two of the domains.

I would like to move the two domains, whose positions are known in both 
conformations, and observe movements in the other two domains.

That would be nice to do steered MD. However, the I need not to pull but 
push the two domains. What do you suggest, what should I try?
I have no experiences in enhanced sampling MD.

I see two potential possibilities:

1. Try pulling with pull-coord1-type: constant-force
This case I might be able to set "negative" force for pulling with 
option pull-coord1-k.

2. Try targeted MD, if gromacs has the possibility to perform it not 
only for the full protein, but for two selections (domains). In addition 
I have seen some posts on targeted MD with gromacs stating that it is 
not a real/best targeted MD implementation. ???

Thanks for your help and suggestions in advance,
Tamas