[gmx-users] Position restraint for 2ns

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

> 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 :)

-Justin

> 
> Rabab Toubar
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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