[gmx-users] input grofile for position restraints

[Anton Feenstra]

"David L. Bostick" wrote:
> 
> I know it is possible to give an additional input gro file for position
> restraints during simulation and that otherwise the initial coordinates in
> the original input file will be taken for the restraints.  Is it possible
> to use this sort of capability for "targeted dynamics?"  In other words, if
> I have say a protein in solvent and wish to impose restraints only on the
> protein backbone to force the protein from one x-ray crystallographically
> determined conformation to another, does the additional gro file giving the
> restraint equilibrium coordinates have to have the same number of particles
> as the entire system?

In short: Yes. The posre.itp file (which should contain a 
[ position_restraints ] section) will determine for which particles
an actual position restraints potential will be defined, so the 
particles which are not mentioned in the position_restraints, will
not get a potential force, but they still must be in the coordinate
file.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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