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

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 30 17:00:32 CET 2012

On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul <jalemkul at 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,


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