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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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