[gmx-users] How to fix Water during simulation ?

[Justin A. Lemkul]

ajani haresh wrote:
> Hello Everyone,
> 
> I am new in Gromacs. I am using gromacs for protein-ligand complex.
> 
> I have few question  ?
> 
> 1): how to fix water during simulation ?
> 

If pdb2gmx wrote the topology, you should be able to invoke "define = 
-DPOSRES_WATER" in the .mdp file.  Check your topology (after the #include 
statement for water) to be sure.

> 2): how to fix protein and ligand during simulation ?
> 

With position restraints.  They will need their own posre.itp files, unless you 
have merged the [moleculetypes], in which case a single posre.itp file is needed.

> 3) how to fix few crystal water molecule during simulation  ?
> 
> 4) how to fix specific water molecule  in simulation ?
> 
> 

Restraining groups of water is tricky.  Position restraints can only be applied 
to individual [moleculetype] directives, so whatever you restrain has to be 
defined as such.  The problem then becomes that you cannot have separate blocks 
of water molecules using the SETTLE algorithm for their constraints.  The same 
problem applies if you using freezegrps in the .mdp file.  You can get around 
this by hacking the topology to include normal constraints for each water 
molecule you're trying to work with.  That becomes a huge pain and will likely 
make you question whether you need to go to all this trouble ;)

Note that freezing and restraining are separate concepts (see the manual and 
webpage).

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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