[gmx-users] Problem with the mdrun_openmpi on cluster

[James Starlight]

For that system I have not defined virtual sites.
BTW the same simulation on local desctop using 2 cores from core2 duo runs OK =)

so one of the solution probably is to try to use more recent gmx 5.0
to see what will happenes

2016-03-14 18:22 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 3/14/16 1:19 PM, James Starlight wrote:
>>
>> I tried to increase size on the system providding much bigger bilayer
>> in the system
>>
>> for this task I obtained another error also relevant to DD
>>
>> Program g_mdrun_openmpi, VERSION 4.5.7
>> Source code file:
>> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_con.c, line: 693
>>
>> Fatal error:
>> DD cell 0 2 1 could only obtain 0 of the 1 atoms that are connected
>> via vsites from the neighboring cells. This probably means your vsite
>> lengths are too long compared to the domain decomposition cell size.
>> Decrease the number of domain decomposition grid cells.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> "It's So Fast It's Slow" (F. Black)
>>
>> Error on node 9, will try to stop all the nodes
>> Halting parallel program g_mdrun_openmpi on CPU 9 out of 64
>>
>>
>> BTW I checked the bottom of the syste,.gro file and found the next
>> sizes which are seems too small for my syste, consisted for several
>> hundreds of lipid, arent it7
>>
>>    15.00000  15.00000  15.00000   0.00000   0.00000   0.00000   0.00000
>>    0.00000   0.00000
>>
>
> No, that seems fine.  But if your box is set up wrong, that's your fault
> from the command below :)
>
>>
>> for my case that gro file was produced automatically using MARTINI method
>>
>> ./insane.py -f test.pdb -o system.gro -p system.top -pbc cubic -box
>> 15,15,15 -l DPPC:4 -l DOPC:3 -l CHOL:3 -salt 0.15 -center -sol W
>>
>>
>> Will be very thankful for any help!!
>>
>
> So you've got a system that is a CG model, with virtual sites?  That's going
> to create all kinds of havoc.  Please do try Googling your error, because
> this difficulty has come up before specifically in the case of CG systems,
> which have longer-than-normal bonded interactions and requires some mdrun
> tuning.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
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