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

[Justin A. Lemkul]

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

-- 
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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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