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

[Mark Abraham]

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,
please?

Mark