[gmx-users] Re: Potential energy from a previous configuration mismatch

Justin Lemkul jalemkul at vt.edu
Fri Nov 30 14:35:25 CET 2012

On 11/30/12 8:21 AM, escajarro wrote:
> I do have constraints, all the bond lengths are fixed and they are specified
> in the topology file. Am I doing something wrong? I copy here the definition
> of one of the models I use. I also tried using in the input the line:
> constraints              = all-bonds
> instead of
> constraints              = none
> with the same result
> <http://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg>

That all looks fine, and the results should be the same under those two 
circumstances.  The problem is likely due to the fact that L-BFGS cannot 
actually make use of constraints (a bug in mdrun), so that is the source of the 
difference.  The EM is being done without constraints, and then the MD starts 
with constraints.  Use a different EM algorithm and see if the outcome improves.



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


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