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
--
========================================
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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