[gmx-users] Water molecule starting at atom x can not be settled - minimization step
ttdtrang at gmail.com
Tue Oct 5 10:11:32 CEST 2010
I checked the initial coordinate file for overlapping atoms, but nothing
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
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
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.
> Many thanks
> 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
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