[gmx-users] Water molecule starting at atom x can not be settled - minimization step

[Justin A. Lemkul]

Trang wrote:
> Dear gmx-users,
> I do a minimization run with this mdp:
> -----------------------------
> constraints         =  none
> ;define              =  -DFLEX_SPC
> integrator          = cg
> ;nstcgsteep         = 300
> emtol               =  100.0
> emstep              =  0.005
> dt                  =  0.001    ; ps !
> nsteps              =  200000  ; total 200 ps.
> nstcomm             =  100
> nstxout             =  10000
> nstvout             =  0
> nstfout             =  0
> nstlog              =  10000
> nstenergy           =  1000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> coulombtype         =  PME ; Reaction-Field
> fourierspacing      =  0.12
> pme_order           =  4
> optimize_fft        =  yes
> ;epsilon_r           =  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             =  Protein  SOL
> tau_t               =  0.01    0.01
> ref_t               =  310     310
> ; Energy monitoring
> energygrps          =  Protein SOL
> ; Isotropic pressure coupling is now on
> Pcoupl              = berendsen
> Pcoupltype          = isotropic
> tau_p               =  0.25
> compressibility     =  5.4e-5
> ref_p               =  1.0
> ; Generate velocites is off at 300 K.
> gen_vel             =  no
> ;gen_temp            =  300.0
> ;gen_seed            =  749261
> 
> ---------------------------
> and get the error, output like this:
> 
> Polak-Ribiere Conjugate Gradients:
>    Tolerance (Fmax)   =  1.00000e+02
>    Number of steps    =       200000
>    F-max             =  4.69437e+04 on atom 2513
>    F-Norm            =  1.05294e+03
> 
> 
> step -1: Water molecule starting at atom 43372 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 
> ...
> 
> Fatal error:
> 1 particles communicated to PME node 4 are more than 2/3 times the 
> cut-off out of the domain decomposition cell of their charge group in 
> dimension y.
> This usually means that your system is not well equilibrated.
> --------------------------
> 
> I did a successful run with another equivalent system (same protein 
> sequence, same number of atoms), even with a LARGER TIMESTEP, 0.002 ps
> I found a lot of people encounter the same error, but in production run 
> step. And in those cases, they're advised to minimize/equilibrate the 
> system more thoroughly. What can I do to resolve this problem in 
> MINIMIZATION step?
> 

You likely have some unresolvable atomic clash(es) in your system that can't be 
energy-minimized.  Check your structure around the location of the problematic 
water molecule to see if anything is overlapping.

-Justin

> Many thanks
> Trang
> 

-- 
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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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