[gmx-users] Tethering

Joanne Hanna J.F.Hanna at warwick.ac.uk
Tue May 17 13:30:13 CEST 2005

Many thanks for this reply.

Would you be able to tell me what the value range is for the position restraints, is 1000 the max? and what do these values mean in terms of the strength or flexibility in the restraint. I have had a look in the manual but could not locate the section relating to the  inference of these values.


Joanne Hanna
Department of Chemistry
University of Warwick

J.F.Hanna at warwick.ac.uk
jfhanna at gmail.com
>>> feenstra at few.vu.nl 05/11/05 12:21 PM >>>
David van der Spoel wrote:

> On Fri, 6 May 2005, Joanne Hanna wrote:
>>Thank you, I had misunderstood what the purpose of the position restraints file. If I have a protein posre.itp and ligand posre.ipt files do i leave them all as seperate files of the same name or do I combine then, also where do i define the force constant and if i have had to make a topology file (which I have had to for an AMP ligand) how do i generate a position restraints file for this?
> there is a utility called genpr

Position restrains, in Gromacs, are a property of a certain molecule 
type, e.g. your protein or the AMP. Each of molecules that you want to 
restrain, will need its own [position_restraints] section. This you 
could add (manually) to the molecule's .top or .itp file, but more 
commonly it is included into the respective file by an '#include' 
statement, like:

-- file protein.top --


protein ...

#ifdef POSRE
#include posre.itp

#include AMP.itp
--- end of file protein.top --

And the AMP.itp would look like:
AMP ...
#ifdef POSRE
#include posre_AMP.itp

The posre*.itp file would look like
1 1 200
2 1 200
3 1 200

Where 1, 2, 3 are the atom numbers to be restrained, i.e. one for each 
atom in your molecule. This may be hundreds or thousands for your 
protein, and several tens for your AMP. Indeed, for this part there is a 
tool called 'genpr' which acccepts an index file and will write a posre 
file for one index group (set of atoms).



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