[gmx-users] adding constraints

Justin A. Lemkul jalemkul at vt.edu
Thu May 20 13:40:35 CEST 2010

subarna thakur wrote:
> Hi all,
> I want to add constraints for bond length of a ligand.Where do I place 
> the constraints statement in the .rtp file or in the .top file? 

Are you looking to constrain only one single bond length?  If so, just add a 
[constraints] section to your topology.  The .rtp file won't do you any good, 
unless you're looking to build a complete .rtp entry and re-process with 
pdb2gmx, but I don't know if [constraints] is a valid entry in an .rtp file.

If you're looking to constrain all bond lengths, leave the topology alone and 
add "constraints = all-bonds" in your .mdp file.


> Subarna Thakur


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list