[gmx-users] GROMACS 4.5.4 keep crashing all the time.

[Justin A. Lemkul]

I concur with what Mark suggested about in vacuo EM.  I would also point out the 
following problem(s):

> and the md.mdp:

Here you call for 300 K as the reference temperature and the temperature at 
which you've equilibrated:

> tc-grps                  = Protein Non-Protein
> tau-t                    = 0.1 0.1  
> ref-t                    = 300 300
> ; Pressure coupling     
> Pcoupl                   = berendsen
> Pcoupltype               = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p                    =  1.0
> compressibility       =  4.5e-5      
> ref_p                 =  1.0           
> ; Generate velocites is on at 290K - do not get velocity from gro file.

And here you're destroying the previous equilibration by re-generating 
velocities and simultaneously generating velocities for the wrong temperature, 
which may or may not induce instability into the system.

> gen_vel             =  yes
> gen_temp            =  290
> gen-seed            =  -1

-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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