[gmx-users] BUG: Free energy calculation

[Michael Shirts]

Sabine, thanks for filing it in redmine!  Having a record helps a lot.
 Can you also attach all your input files to the redmine filing?  It
can only really be debugged if the input files you used are included.

Best,
Michael
On Fri, Mar 23, 2012 at 9:11 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Sabine Reisser wrote:
>>
>> Hi Mark,
>>
>> with FE, without PR : same error
>> without FE, with PR: stable
>> without FE, without PR: stable
>>
>> I've never had this error before.
>>
>> Logfile says:
>> [...]
>> Initializing Domain Decomposition on 2 nodes
>> Dynamic load balancing: no
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>    two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761
>>  multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686
>> Minimum cell size due to bonded interactions: 3.675 nm
>> Using 0 separate PME nodes
>> Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm
>> The maximum allowed number of cells is: X 1 Y 1 Z 2
>> Domain decomposition grid 1 x 1 x 2, separate PME nodes 0
>> PME domain decomposition: 2 x 1 x 1
>> Domain decomposition nodeid 0, coordinates 0 0 0
>> [...]
>> Linking all bonded interactions to atoms
>> There are 55376 inter charge-group exclusions,
>> will use an extra communication step for exclusion forces for PME
>>
>> The initial number of communication pulses is: Z 1
>> The initial domain decomposition cell size is: Z 5.09 nm
>>
>> The maximum allowed distance for charge groups involved in interactions
>> is:
>>                 non-bonded interactions           1.200 nm
>>            two-body bonded interactions  (-rdd)   4.213 nm
>>          multi-body bonded interactions  (-rdd)   4.213 nm
>>
>>
>
> These quantities look very weird to me.  They indicate interactions that are
> very far apart are influencing one another.  Can you provide a complete .mdp
> file?  It seems like some aspect of the free energy settings (perhaps
> couple-intramol?) and DD aren't getting along.  The other possibility is to
> try particle decomposition instead of DD (i.e. mdrun -pd).
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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