On 11/30/12 11:00 AM, Mark Abraham wrote:
On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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<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.
If L-BFGS is silently not using the constraints, then I think that is a
real bug and it would be good to report it so we might sometime fix it. Or
maybe it's an undocumented "feature" we need to document? Which is it,
please?
From the recent discussion, it seems that L-BFGS is silently ignoring the
constraints, as Berk observed there is no check for this combination, which
explained David's finding that bond lengths seem to vary randomly:
http://lists.gromacs.org/pipermail/gmx-developers/2012-November/006433.html
-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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