[gmx-users] Constraints

[Anton Feenstra]

"Tanos C. C. França" wrote:
> 
>         Hi all again,
>         How should I do to perform a minimization with constraints ? Is it enough
> just typing what I wanna constraint in the "constraint" option in the
> "em.mdp" file  ? If so, are the options like in other packages (hydrogens,
> side chain, backbone, heavy atoms, etc ...) ? Or should I type something
> different ?

No, the constraint option is for constraining bond lengths.

You probably want position restraints. By default, pdb2gmx generates
a posre.itp for all heavy atoms in your protein. If not, or if you
want to position restrain a different set of atoms, you can make one 
yourself. The file is simply a list of atom numbers and force 
constants, like:

[ position_restraints ]
; atom  type      fx      fy      fz
     1     1    1000    1000    1000
     5     1    1000    1000    1000
     6     1    1000    1000    1000
     7     1    1000    1000    1000

Note that position restraints work on a molecule basis, so the atom
numbers you need are those used in the corresponding section(s) of
your .top (and/or .itp) files. E.g. for restraining the water oxygens,
you need :
[ position_restraints ]
; atom  type      fx      fy      fz
     1     1    1000    1000    1000

Which will constrain *all* water oxygens. Also, the [ position_restraints ]
directive needs to be inside the corresponding [ moleculetype ] section
in your topology.

>         Another question I have is how to perform in GROMACS a energy minimization
> in vacuo with a distance dependent dielectric constant of water (78,54) and
> 1 - 4 interactions scaled by a factor of 0,5 .  Is that possible ?

I don't think we have distance dependent dielectric constant in Gromacs.
I also don't think you can scale 1-4's separate from other interactions.
Check the .mdp file options page in the online manual.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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