Fwd: [gmx-users] Generation of the Distance Restraints

Wed Mar 14 17:08:11 CET 2012

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 :(

James

14 марта 2012 г. 19:43 пользователь Justin A. Lemkul <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 | (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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