[gmx-users] segmentation fault.

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> dear gmx-users,
>                          During equilibriation i get the following 
> error.Any suggestions please.
> 
> *grompp*
> 
> WARNING 1 [file npt.mdp]:
>   The sum of the two largest charge group radii (2.369582) is larger than
>   rlist (1.000000)
> 
> 

This message suggests your topology is somehow broken.

> This run will generate roughly 73 Mb of data
> 
> There was 1 warning
> 
> Back Off! I just backed up npt.tpr to ./#npt.tpr.5#
> 
> gcq#113: "I Don't Like Dirt" (The Breeders)
> 
> *
> mdrun*
> 
> WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg 
> the forces deviate on average -2147483648% from minus the numerical 
> derivative of the potential
> 
> 
> WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg 
> the forces deviate on average -2147483648% from minus the numerical 
> derivative of the potential
> 

This still indicates a problem with the table.  Take Chris' advice and try your 
simulation without tabulated potentials.  This will tell you whether the problem 
is from a bad starting structure or because your tables are somehow not usable.

> Making 1D domain decomposition 2 x 1 x 1
> 
> Back Off! I just backed up npt.trr to ./#npt.trr.6#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.23#
> starting mdrun 'NA SODIUM ION in water'
> 50000 steps,     50.0 ps.
> 
> step 0: Water molecule starting at atom 6153 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 
> Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.23#
> 
> step 0: Water molecule starting at atom 4410 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 
> Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.23#
> 
> Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.23#
> 
> Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.23#
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> *Segmentation fault*
> 

Step 0 failures indicate either (1) your starting configuration is unreasonable, 
(2) your .mdp settings are inappropriate, or (3) the tabulated potential is 
causing the system to collapse.  Did you do energy minimization?  Was it 
successful?  Good EM is the way around point 1.

> *mdp file*
> title           = nacl                          
> define          = -DPOSRES      ; position restrain the protein

What are you restraining?

<snip>

> tc-grps         = SOL Na Cl     ; two coupling groups - more accurate

Never couple solvent and ions separately.  This alone can be a reason for 
instability.

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do

-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

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