[gmx-developers] distance_restraints and domain decomposition

[andrea spitaleri]

Hi Berk,
thanks for your answer. In effect, in my case averaging over 4 atoms pairs is not necessary since
my purpose is to keep fixed my ion. Splitting in 8 restraints the run goes fine with 64 cpus.

Thanks a lot

regards,


andrea

Berk Hess wrote:
> Hi,
> 
> You are averaging over multiple pairs (4) within 2 restraints (index 0 
> and 1).
> This is not supported (yet) with DD.
> 
> Are you sure you want to average over 4 atom pairs within one restraint
> and not use 4 separate restraints?
> 
> Berk
> 
> andrea spitaleri wrote:
>> Hi there,
>> I am facing a problem with the domain decomposition and distance_restraints. My system is a protein
>> with Zn ions and in order to keep the ion in the right position, i use distance_restraints in my
>> topology:
>>
>> [distance_restraints]
>> ;ai aj type index type' low up1 up2 fac
>>
>> 613  98 1   0   1   0.18 0.30 0.35 5
>> 613 119 1   0   1   0.18 0.30 0.35 5
>> 613 274 1   0   1   0.18 0.30 0.35 5
>> 613 300 1   0   1   0.18 0.30 0.35 5
>> 614 479 1   1   1   0.18 0.30 0.35 5
>> 614 219 1   1   1   0.18 0.30 0.35 5
>> 614 198 1   1   1   0.18 0.30 0.35 5
>> 614 450 1   1   1   0.18 0.30 0.35 5
>>
>> Now, the run goes fine using one single cpu but as soon I ask for a parallel run I get this error:
>>
>> Initializing the distance restraints
>> NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this
>> is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option
>> -pd)
>>
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.0.3
>> Source code file: disre.c, line: 135
>>
>> Fatal error:
>> Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain
>> decomposition, use particle decomposition (mdrun option -pd)
>>
>> If I use -pd option, the run goes fine but dramatically slowly (days instead of hour).
>>
>> My distances are all below the cut-off (~ 0.21).
>> I found only one post (http://www.gromacs.org/pipermail/gmx-users/2008-December/038507.html) with
>> probably a bugzilla submission suggestion but I could not find any answer to it.
>>
>> Any help?
>>
>> Thanks in advance for your help
>>
>> Regards
>>
>> andrea
>>
>>
>>
>>
>>   
> 
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-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
-------------------------------

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