[gmx-users] steered MD

[chris.neale at utoronto.ca]

> Dear users,
>
> I would like to carry out steered molecular dyanmics simulations on one of
> my protein dimer. I have a few questions to learn regarding this.
>
> 1. The mdrun program needs -pn index.ndx file
>
> The way I understand is, we need to create the index file with groups (say
> atom1 to which the spring has to be attached and the atom 2 which I would
> like to fix). These are the names (I mean what ever the names I give for the
> groups in the index file) do I need to mention at group_1 and group_2 in
> pull.ppa ??

yes, read the manual.

I believe the index file can be prepared in the same way as we
> do in conventional MD simulations.

yes, in fact if you put group0 and group1 in your original .ndx file  
then you can use the same .ndx for -n and -pn

>
> 2. Its a general question. What usually the rates people does use for spring
> motions ?

As slow as possible while still finishing the simulation within a  
reasonable amount of time.

>
> 3. I donot have experimental AFM studies on my system so how can I choose
> the optimum force ?

That depends on your system and it's properties. I don't know of any  
general rule. I suggest that you try 500 kcal/mol/nm^2 with a fairly  
quick pulling (finish in one day of run-time?) and see if you do  
eventually obtain your target end state. If you do, then the Fc is  
probably high enough.

>
> 4. I want to pull the atom along the "Z" direction. I belive afm_dir1 = 0 0
1

Yes.

>
> 5. How can I mention the initial spring positoins ?? i.e., afm_init1 ??
>
> I looked for a few tutorials on this but i do not have any luck. If somebody
> finds some stuff regarding this could you please share the links with me ??

The manual gives you all of this information. Check the online manual  
under .mdp options for a quick description.

>
> Thanks.

You are clearly using gromacs 3. Please note that gromacs 4 has a  
different input parameter method (but you can read the manual to see  
differences when you get to gmx 4).