On 14/10/2010 12:09 PM, Justin A. Lemkul wrote:
Spitaleri Andrea wrote:
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<http://www.sanraffaele.org/grazieate>
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Hi there,
this is a very old issue for me at lest and I still get error running
a remd simulation using restraints for ion. I am using gmx4.0.7
This is my input:
; Distance restraints
disre = simple
disre_weighting = equal
disre_fc = 1000
and in topol.top
[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
957 309 1 0 1 0.18 0.20 0.25 1
957 338 1 1 1 0.18 0.20 0.25 1
957 701 1 2 1 0.18 0.20 0.25 1
957 733 1 3 1 0.18 0.20 0.25 1
956 149 1 4 1 0.18 0.20 0.25 1
956 185 1 5 1 0.18 0.20 0.25 1
956 417 1 6 1 0.18 0.20 0.25 1
956 462 1 7 1 0.18 0.20 0.25 1
So all different restraints. My input run is:
#PBS -l nodes=120
mpirun mdrun_d -s remd -v -deffnm remd -multi 5 -replex 5000 -npme 8
-dd 4 4 1
and immediately I get:
Program mdrun_d, VERSION 4.0.7
Source code file: disre.c, line: 143
Fatal error:
Time or ensemble averaged or multiple pair distance restraints do not
work (yet) with domain decomposition, use particle decomposition
(mdrun option -pd)
That's strange since I am not neither using time nor ensemble
averages nor multiple dist restraints.
You are using ensemble averaging, which is invoked when combining
"disre = simple" and mdrun -multi, per the manual. You should be able
to use mdrun -pd, as the error message suggests.
That is, "disre = simple" and mdrun -multi combine to implement ensemble
averaging. This seems not to be what the OP wanted, which seemed to be
distance restraints with REMD. Other than using PD, there's no
work-around in 4.0.x or current code.
Mark
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