[gmx-users] No domain decomposition

[Justin Lemkul]

On 9/24/15 8:02 AM, soumadwip ghosh wrote:
> Thanks Tsjerk for your help. But I started the mdrun using the command
> mdrun -deffnm em -nt 8 and it gave the following outcomes.
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Warning: 1-4 interaction between 1544 and 1554 at distance 3.261 which is
> larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> step 31: Water molecule starting at atom 63649 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> step 34: Water molecule starting at atom 46552 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> step 35: Water molecule starting at atom 46552 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> step 37: Water molecule starting at atom 64213 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> step 38: Water molecule starting at atom 46045 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to Fmax < 1000 in 1568 steps
> Potential Energy  = -1.7034508e+06
> Maximum force     =  9.5823822e+02 on atom 1546
> Norm of force     =  1.3556979e+01
>
> As you can see the files have been created but I get the above warnings
> hinting at the system blowing up. I have taken the em.gro file and did an
> NVT for 100 ps with 0.001 timestep and it resulted is segmentation faults
> as below.
>
> step 675: Water molecule starting at atom 43849 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Segmentation fault (core dumped)
>
> What should I do? Was the command used for mdrun ( -nt 8) wrong? Am I
> missing something important. Your help will be appreciated.
>

All of the evidence (your previous message related to the DD problems and this 
one) suggests something wrong with the topology.  The .log file will tell you 
the lengths of the interactions used for the DD cell construction, so check that 
information carefully as it may indicate a problem with bonded connectivity. 
How does the minimized structure look?  Any obvious distortions?

-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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