[gmx-users] How to specify .mdp file for position restrained simulation?

[Mark Abraham]

Peggy Yao wrote:
> Hi,
> 
> How to specify the .mdp file in order to run position restrained
> simulation? From the examples I found on the internet, it seems that
> the only difference between the .mdp file for position restrained
> simulation and the one for actual MD simulation is the simulation time
> -- the position restrained simulation is much shorter. 

Use diff first.mdp second.mdp. I bet the "define = " line is different. 
See http://wiki.gromacs.org/index.php/Include_File_Mechanism for clues 
how this works.

> Is this
> observation true in general?

Well yes, but it's not diagnostic :-) The point of the PR simulation is 
to guide the system towards chemical equilibrium with your structures of 
interest near to some arrangement you'd like to have near the start of 
your data collection. You then turn off PR and start collecting data 
some time after that.

> If yes, usually, how long is enough for the position restrained simulation?

That's system-dependent and hard to judge anyway. Check literature for 
preparation protocols for systems similar to yours.

> If not, how to specify the .mdp file for position restrained simulation then?

Follow my advice in the last few emails and you'll have more of a clue.

Mark