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

[Itamar Kass]

Hi Justing,

I had reinitialised the systems after the PR run but I don't think this is the origin of the error. Because the system with the Ca crashed allways in the PR state, although the systems run with 4.0.7 done it fine.

Best,
Itamnar

On 18/08/2011, at 10:39 AM, Justin A. Lemkul wrote:

> 
> 
> 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
> 
> -- 
> ========================================
> 
> 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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"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

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| Itamar Kass, Ph.D.
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