[gmx-users] Making easy position restrain

Xavier Periole x.periole at chem.rug.nl
Fri Nov 5 12:53:24 CET 2004

Hector Martinez-Seara Monne wrote:

> Hi all,
> sorry in advance for the question because I'm sure it's not the first 
> time that has been posted but I haven't been able to find it (also the 
> manual gives a short example but not enough for allow me to completely 
> understand how to use it). I just want to know if there's any easy way 
> to define positions restrains over all the atoms of a type instead to 
> number all one by one. If yes can you tell me how?. For example 
> imagine I have a box of SPC water and I want to fix all oxygens ( this 
> is very related with one of the questions I've read today) or I want 
> to fix all the heads of a monolayer in a plane during the equilibration
 From the way position restraint work you have to give a posre.itp file 
to grompp. This file has to contain
the list of the atom (number) that you want to apply the restrain on and 
its index number. The fact is that
the restrains have to defined for each molecule type. In the case of the 
water exemple the posre.itp would
contain the index number of oxygen (3) and the x, y and z restrain force 
(1000 1000 1000 by default).

You have to define an index (make_ndx) containing the atoms (type if you 
wish) that will feel the restrain
and give it to genpr -conf.gro -n index to generate the posre.itp 
corresponding to the given molecule. Remember
that you do not define the position restain based on the conf.gro but on 
the topology of each molecule.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

More information about the gromacs.org_gmx-users mailing list