[gmx-users] Position restraint for 2ns

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 2 19:19:12 CEST 2010

Rabab Toubar wrote:
> Hi,
> I am trying to reproduce some steps from a  paper, the authors set 
> position restraint to the protein (all-bonds) with a force constant of 
> 1000 for 2ns.

Constraints and restraints are different things in Gromacs, so setting position 
restraints is done independently of constraining bond lengths.


> I edited the pr.md file  where nsteps would result in 2 ns, and I 
> searched the mailing list and knew that the force cons is 1000 by 
> default if we define -DPOSRES
> My question is the run ended very quickly that doesn't seem 2ns for me. 
> I apologize if it is a silly question but I have just strated using GMX
> Thanks

Well, what does the log file say?  What does gmxcheck tell you about your 
trajectory and/or energy files?  I don't know what you mean by saying it 
"doesn't seem" like your trajectory is complete.  GROMACS is known for begin fast :)


> Rabab Toubar


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