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

[Mark Abraham]

----- Original Message -----
From: Trang <ttdtrang at gmail.com>
Date: Tuesday, October 5, 2010 19:12
Subject: Re: [gmx-users] Water molecule starting at atom x can not be settled	- minimization step
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> I checked the initial coordinate file for overlapping atoms, but nothing found.

Even for the water at atom index 43372?

> 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 don't understand your meaning. A molecule can have more than one position, an atom can't.
  
> 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?

Using constraints during EM is not always a great idea, since the point of the procedure is to let atoms move according to the forces to relax bad contacts. Once the EM completes, the waters will be close to the geometry enforced by the constraint, which your first constraint-activated MD step will then enforce. Thus, try uncommenting your "define="-DFLEXSPC" line.

Mark

> 
> 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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