[gmx-developers] distance_restraints and domain decomposition

[andrea spitaleri]

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




-- 
-------------------------------
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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