Fwd: [gmx-users] Generation of the Distance Restraints
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 14 17:26:25 CET 2012
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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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