[gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

[Justin A. Lemkul]

Simone Cirri wrote:
> Justin A. Lemkul wrote:
> 
>     ; Berendsen temperature coupling is on in three groups
>     Tcoupl              =  berendsen
> 
>     tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+
> 
>     ref_t               =  300      300     300
> 
>     Never couple solvent and ions separately. Surely grompp warned you
>     that you should be using "Protein Non-Protein"? See here:
> 
>     http://www.gromacs.org/Documentation/Terminology/Thermostats
> 
> 
> Hi Justin, thanks for the suggestion. Actually, it's an error I've 
> always been doing and I'm glad I've solved it.
> However, I'm afraid it has nothing to do with the problem, because I 
> just tried to run the MD again (after modifying the md.mdp as you told 
> me) and the fatal error is still there.
> I've noticed the the T-coupling mistake is also in pr.mdp. Do you think 
> that correcting it and re-running the PR simulation would fix the "water 
> molecule can not be settled" problem?

It's probably worth a shot.  It's not appropriate to couple solvent and ions 
separately in any phase, equilibration or data collection.

-Justin

> Anyway here is the pr.mdp (as it was before):
> 
> title               =  hsacyx
> warnings            =  10
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  100000    ; total 200.0 ps.
> nstcomm             =  1
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype        =  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing        =  0.12
> fourier_nx        =  0
> fourier_ny        =  0
> fourier_nz        =  0
> pme_order        =  6
> ewald_rtol        =  1e-5
> optimize_fft        =  yes
> ; Berendsen temperature coupling is on in four  groups
> Tcoupl              =  berendsen
> tau_t               =  0.1     0.1    0.1
> tc-grps            =  Protein     SOL    NA+
> ref_t               =  300     300    300
> ; Pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> Thank you
> 
> Simone Cirri
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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