[gmx-users] position restrained minimization on the one part of a system

[Mark Abraham]

On 26/10/2011 11:24 PM, Atila Petrosian wrote:
> Dear all
>
> my system contains protein + ligand+ water molecules.
>
> protein + ligand = solute
>
> water molecules = solvent
>
> I want to do minimization energy in 3 steps :
>
> step 1) on protein only
>
> step 2) on all solute (protein + ligand)
>
> step 3) on all system
>
> should I use position restrained minimization energy and use define =  
> -DPOSRES in mdp file?

You will need some way to change which [moleculetypes] have position 
restraints during which step. The details will vary with how you've 
constructed your overall topology. IIRC, if pdb2gmx is able to treat the 
whole system in one pass, then it will write such position restraint 
files automatically. Otherwise, you will have to understand how the 
#include mechanism works and how to trigger it with define = -Dxxxxx. By 
design, it is possible to use the same .top for all three steps.

> if so, what is my mdp file for each of 3 steps?

Each will use a different "define" line - check out some tutorials for 
example ideas.

>
>
> # step 1:
>
> ??? please complete this section.
>
> # step 2:
>
> define  = -DPOSRES_WATER
>
> # step 3:
>
> I don't use -DPOSRES.
>
>
> In posre.itp file, what is suitable value for force constant?

Whatever leads to successful equilibration. The default used by pdb2gmx 
is 1000 (whatever the units are).

Mark