[gmx-users] Segmentation fault

[Justin A. Lemkul]

Sayan Bagchi wrote:
> Hello All,
> 
> I was trying to run a MD simulation of a 17 amino acid peptide. At the 
> position restraint step, the program crashed after running ~536 ps.
> 
> It gave the error message:
> 
> "t=536.242 ps: Water molecule starting at atom 6101 cannot be settled.
> Check for bad contacts and/or reduce the timestep. Wrote pdb files with 
> previous and current coordinates."
> 
> So I looked into the pdb files for atom 6101:
> 
> In the last but one step, the pdb file looks like:
> 
> ATOM   6101  OW  SOL  1970      44.896  30.613  17.849  1.00  0.00
> ATOM   6102  HW1 SOL  1970      45.375  30.296  18.668  1.00  0.00
> ATOM   6103  HW2 SOL  1970      44.264  29.904  17.537  1.00  0.00
> 
> In the last step, the pdb file looks like:
> 
> ATOM   6101  OW  SOL  1970    
> 395154652137521152.000-290190255628222464.000695407981780533248.000  
> 1.00  0.00
> ATOM   6102  HW1 SOL  1970    
> -2104656020830683136.0005806908484133847040.000-6427192471385538560.000  
> 1.00  0.00
> ATOM   6103  HW2 SOL  1970    
> 1131095442881249280.000593978790032441344.0001018902650772520960.000  
> 1.00  0.00
> 
> So, there is clearly something wrong. What should I do now to solve this 
> problem?
> 

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

-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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