James Starlight wrote:
Justin,
The whole error was
Reading file md_rest1.tpr, VERSION 4.5.5 (single precision)
NOTE: atoms involved in distance restraints should be within the longest
cut-of$
-------------------------------------------------------
Program mdrun_mpi_d.openmpi, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/disre.c, line: 143
Fatal error:
Time or ensemble averaged or multiple pair distance restraints do not
work (yet$
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Gabba Gabba Hey!" (The Ramones)
Error on node 5, will try to stop all the nodes
Halting parallel program mdrun_mpi_d.openmpi on CPU 5 out of 12
-------------------------------------------------------
and so on for each CPU :)
Might it be with some PME order ? I've recieved errors about wrong PME
order when tried to lauch my simulations on big ammoun of the nodes but
could not find possible way to fix it :(
The error you're receiving is the one I posted before. For some reason it's not
being printed correctly. You need to be using mdrun -pd for your simulation to
work. You can't use DD with all those restraints.
-Justin
James
14 марта 2012 г. 19:43 пользователь Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> написал:
James Starlight wrote:
Mark,
My restrains on topology consist of the next section
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
; Chi N - CA - CB - CG
2908 2910 2911 2912 1 1 180 0 1 2
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1097 3201 1 1 1 0.796 0.841 0.900 1.0
2948 3201 1 2 1 0.796 0.841 0.900 1.0
1097 2948 1 3 1 0.796 0.841 0.900 1.0
1097 2999 1 4 1 0.800 1.000 1.100 1.0
1098 2034 1 5 1 0.800 1.000 1.100 1.0
1098 2042 1 6 1 0.800 1.000 1.100 1.0
1098 2067 1 7 1 0.800 1.000 1.100 1.0
1130 3241 1 8 1 0.540 0.630 0.700 1.0
546 3393 1 9 1 1.162 1.725 1.800 1.0
628 3460 1 10 1 1.438 2.067 2.100 1.0
637 3460 1 11 1 0.700 1.238 1.300 1.0
648 2791 1 12 1 1.788 2.152 2.200 1.0
648 3376 1 13 1 1.736 2.061 2.150 1.0
2292 2743 1 14 1 0.200 0.300 0.350 1.0
1258 2203 1 15 1 0.200 0.300 0.350 1.0
Also I've attached my md.mdp file.
I have no problems with that system on my home desktop.
On cluster with installed MPI I've lunch my simulation by means
of below command
grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx
-o md_50ns.tpr
mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm md_50ns
I'll be very thankful if you show me what's wrong could be with
my initial systems because I have no any problems with my
systems on my home desktop. On the other hand on Cluster some of
my jobs ends with the errors ( something wrong with PME order or
the error wich I've shown you with the ensembles of restrains)
It was installed the same last version of Gromacs on cluster
like on my desctop ( difference only in double precission with
lack on my home desctop but present on cluster)
Could you tell me in what log files I could obtain more detailed
information of the source of such erors? I've checked only
md.log as well as name_of_the_simulation.log. Besides there are
files gromacs.err wich contain information about crashed simulation.
You didn't include the whole error in your first message, which
should read "Time or ensemble averaged or multiple pair distance
restraints do not work (yet) with domain decomposition, use particle
decomposition (mdrun option -pd)"
Thus the error message tells you how to proceed.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
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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