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

[Trang]

I checked the initial coordinate file for overlapping atoms, but nothing
found.
I checked the step*.pdb file written after each crash but did not really
understand those coordinates, for the problematic molecules have MORE THAN 1
positions in those files. what does that mean?

I tried to reproduce the error on another computer, and it could be
reproduced.

I think I should check the initial coordinate more thoroughly to find all
likely problematic points. Would you please recommend a way for me to do
that check?

Thanks
Trang

On Thu, Sep 30, 2010 at 5:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
> --
> ========================================
>
> 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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