[gmx-users] Water molecule near protein surface cannot be settled.

Dawid das addiw7 at googlemail.com
Tue Aug 12 11:54:30 CEST 2014 

Actually, I managed to minimize my system. What I did was 2000 steps of
minimization using l-bfgs algorithm and starting from obtain geometry it
took ca. 600 steps using conjugate gradient algorithm.


2014-08-11 21:56 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> If you search, Justin has posted suggested CHARMM non-bonded setups many
> times on this list. For choosing a simulation algorithm, ou need to think
> about what you are trying to model...
>
> Mark
>
>
> On Mon, Aug 11, 2014 at 6:24 AM, Dawid das <addiw7 at googlemail.com> wrote:
>
> > Okey, can I have one more question? Are there any information what
> settings
> > (e.g. cut-off values, temperature coupling, algorithms, etc.) I should
> use
> > with my CHARMM27 force field for the best results?
> >
> >
> > 2014-08-11 14:03 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 8/11/14, 9:01 AM, Dawid das wrote:
> > >
> > >> Actually if you suggest that this problem is due to topological
> > >> instability
> > >> maybe it is important to say that I did not get this problem when I
> did
> > >> not
> > >> use genion to add 0.15 mM solution of NaCl to the system.
> > >>
> > >>
> > > Then investigate where the ions have been added.  The randomness of
> that
> > > process can occasionally lead to bad contacts.  Regardless, mdrun is
> > > telling you where the problem is so it should be easy to spot if this
> is
> > > the case.
> > >
> > > -Justin
> > >
> > >
> > >
> > >> 2014-08-11 13:55 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> > >>
> > >>
> > >>>
> > >>> On 8/11/14, 8:43 AM, Dawid das wrote:
> > >>>
> > >>>  That's what happens next:
> > >>>>
> > >>>> step -1: Water molecule starting at atom 16281 can not be settled.
> > >>>> Check for bad contacts and/or reduce the timestep if appropriate.
> > >>>>
> > >>>> step -1: Water molecule starting at atom 27936 can not be settled.
> > >>>> Check for bad contacts and/or reduce the timestep if appropriate.
> > >>>> Wrote pdb files with previous and current coordinates
> > >>>> Wrote pdb files with previous and current coordinates
> > >>>>
> > >>>> step -1: Water molecule starting at atom 4074 can not be settled.
> > >>>> Check for bad contacts and/or reduce the timestep if appropriate.
> > >>>>
> > >>>> Back Off! I just backed up step-1b_n0.pdb to ./#step-1b_n0.pdb.1#
> > >>>>
> > >>>> Back Off! I just backed up step-1c_n0.pdb to ./#step-1c_n0.pdb.1#
> > >>>> Wrote pdb files with previous and current coordinates
> > >>>>    Step 42, Epot=-4.159425e+05, Fnorm=5.172e+02, Fmax=2.777e+04
> (atom
> > >>>> 1726)
> > >>>>
> > >>>> step -1: Water molecule starting at atom 16281 can not be settled.
> > >>>> Check for bad contacts and/or reduce the timestep if appropriate.
> > >>>>
> > >>>> step -1: Water molecule starting at atom 31338 can not be settled.
> > >>>> Check for bad contacts and/or reduce the timestep if appropriate.
> > >>>>
> > >>>> Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.1#
> > >>>>
> > >>>> Back Off! I just backed up step-1b_n0.pdb to ./#step-1b_n0.pdb.2#
> > >>>>
> > >>>> Back Off! I just backed up step-1c_n0.pdb to ./#step-1c_n0.pdb.2#
> > >>>>
> > >>>> Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.1#
> > >>>> Wrote pdb files with previous and current coordinates
> > >>>> Wrote pdb files with previous and current coordinates
> > >>>> mpiexec: process_obit_event: evt 4 task 0 on wn656 stat 267.
> > >>>> mpiexec: wait_tasks: waiting for wn656.
> > >>>> mpiexec: kill_others_now: alarm went off, killing all other tasks.
> > >>>> mpiexec: kill_tasks: killing all tasks.
> > >>>> mpiexec: process_kill_event: evt 6 task 1 on wn656.
> > >>>> mpiexec: process_obit_event: evt 5 task 1 on wn656 stat 265.
> > >>>> mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
> > >>>> mpiexec: Warning: task 1 died with signal 9 (Killed).
> > >>>>
> > >>>>
> > >>>> And that's what's happening for steepest descent algorithm:
> > >>>>
> > >>>> Step=   14, Dmax= 1.1e-01 nm, Epot= -3.85410e+05 Fmax= 2.96998e+05,
> > >>>> atom=
> > >>>> 1726
> > >>>> Step=   15, Dmax= 1.3e-01 nm, Epot= -3.86977e+05 Fmax= 6.09612e+04,
> > >>>> atom=
> > >>>> 1726
> > >>>>
> > >>>> step 16: Water molecule starting at atom 3774 can not be settled.
> > >>>> Check for bad contacts and/or reduce the timestep if appropriate.
> > >>>> Wrote pdb files with previous and current coordinates
> > >>>> Step=   16, Dmax= 1.5e-01 nm, Epot= -1.61388e+23 Fmax=         inf,
> > >>>> atom=
> > >>>> 1326
> > >>>> Step=   17, Dmax= 1.8e-01 nm, Epot= -3.93744e+05 Fmax= 2.75780e+04,
> > >>>> atom=
> > >>>> 1728^MStep=   18, Dmax= 9.2e-02 nm, Epot= -3.93744e+05 Fmax=
> > >>>> 2.75780e+04,
> > >>>> atom= 1728^MStep=   19, Dmax= 4.6e-02 nm, Epot= -3.93744e+05 Fmax=
> > >>>> 2.75780e+04, atom= 1728^MStep=   20, Dmax= 2.3e-02 nm, Epot=
> > >>>> -3.93744e+05
> > >>>> Fmax= 2.75780e+04, atom= 1728^MStep=   21, Dmax= 1.2e-02 nm, Epot=
> > >>>> -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=   22, Dmax=
> 5.8e-03
> > >>>> nm,
> > >>>> Epot= -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=   23, Dmax=
> > >>>> 2.9e-03
> > >>>> nm, Epot= -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=   24,
> > Dmax=
> > >>>> 1.4e-03 nm, Epot= -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=
> > >>>> 25,
> > >>>> Dmax= 7.2e-04 nm, Epot= -3.93744e+05 Fmax= 2.75780e+04, atom=
> > >>>> 1728^MStep=
> > >>>> 26, Dmax= 3.6e-04 nm, Epot= -3.93744e+05 Fmax= 2.75780e+04, atom=
> > >>>> 1728^MStep=   27, Dmax= 1.8e-04 nm, Epot= -3.93744e+05 Fmax=
> > >>>> 2.75780e+04,
> > >>>> atom= 1728^MStep=   28, Dmax= 9.0e-05 nm, Epot= -3.93744e+05 Fmax=
> > >>>> 2.75780e+04, atom= 1728^MStep=   29, Dmax= 4.5e-05 nm, Epot=
> > >>>> -3.93744e+05
> > >>>> Fmax= 2.75780e+04, atom= 1728^MStep=   30, Dmax= 2.3e-05 nm, Epot=
> > >>>> -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=   31, Dmax=
> 1.1e-05
> > >>>> nm,
> > >>>> Epot= -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=   32, Dmax=
> > >>>> 5.6e-06
> > >>>> nm, Epot= -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=   33,
> > Dmax=
> > >>>> 2.8e-06 nm, Epot= -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^MStep=
> > >>>> 34,
> > >>>> Dmax= 1.4e-06 nm, Epot= -3.93744e+05 Fmax= 2.75780e+04, atom= 1728^M
> > >>>> Stepsize too small, or no change in energy.
> > >>>> Converged to machine precision,
> > >>>> but not to the requested precision Fmax < 500
> > >>>>
> > >>>> Double precision normally gives you higher accuracy.
> > >>>> You might need to increase your constraint accuracy, or turn
> > >>>> off constraints alltogether (set constraints = none in mdp file)
> > >>>>
> > >>>> writing lowest energy coordinates.
> > >>>>
> > >>>> Steepest Descents converged to machine precision in 35 steps,
> > >>>> but did not reach the requested Fmax < 500.
> > >>>> Potential Energy  = -1.6138844e+23
> > >>>> Maximum force     =            inf on atom 1326
> > >>>> Norm of force     =            inf
> > >>>>
> > >>>> gcq#252: "It's Coming Right For Us !" (South Park)
> > >>>>
> > >>>> mpiexec: process_obit_event: evt 4 task 0 on wn502 stat 0.
> > >>>> mpiexec: process_obit_event: evt 5 task 1 on wn502 stat 0.
> > >>>>
> > >>>>
> > >>>> So it seems to me that these energy and force values are not
> > reasonable.
> > >>>>
> > >>>>
> > >>>>  Infinite forces never are :)  The result suggests topological
> > >>> instability
> > >>> to me.  The SETTLE warnings are likely not the problem, they are the
> > >>> symptom of something else.  Investigate atom 1326 as is indicated by
> > >>> mdrun.
> > >>>   Beyond that, the advice at http://www.gromacs.org/
> > >>> Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System is
> > >>> your best bet.
> > >>>
> > >>> -Justin
> > >>>
> > >>>
> > >>>
> > >>>  2014-08-11 13:18 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> > >>>>
> > >>>>
> > >>>>
> > >>>>> On 8/11/14, 8:17 AM, Dawid das wrote:
> > >>>>>
> > >>>>>   What do you mean by this question? Do you suggest to try
> > >>>>> reoptimization
> > >>>>>
> > >>>>>> starting from previous coordinates?
> > >>>>>>
> > >>>>>>
> > >>>>>>   You posted a SETTLE warning from step -1 during EM, but did not
> > >>>>>>
> > >>>>> indicate
> > >>>>> if the EM proceeded and finished.  That's what I'm asking.  What
> > >>>>> happened
> > >>>>> next?  Did EM finish?  Did it yield a sensible energy and maximum
> > >>>>> force?
> > >>>>>
> > >>>>> -Justin
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>   2014-08-11 12:36 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> > >>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>  On 8/11/14, 5:40 AM, Dawid das wrote:
> > >>>>>>>
> > >>>>>>>    I forgot to mention that I get similar error for steepest
> > descent
> > >>>>>>>
> > >>>>>>>  minimization, not only conjugate gradient. Shall I change some
> > >>>>>>>> options
> > >>>>>>>> in
> > >>>>>>>> *mdp files?
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>    Does minimization proceed, i.e. the SETTLE problem is
> resolved?
> > >>>>>>>>   It's
> > >>>>>>>>
> > >>>>>>>>  not
> > >>>>>>> uncommon to see such messages in the very early stages of EM.  If
> > >>>>>>> they
> > >>>>>>> resolve and the energy and force values are sensible, there's no
> > real
> > >>>>>>> problem.
> > >>>>>>>
> > >>>>>>> -Justin
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>    2014-08-11 10:32 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>>     Dear Gromacs experts,
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>  I have encountered quite annoying problem again. When I try
> > either
> > >>>>>>>>> minimization or NVT dynamics of my solvated protein system I
> get
> > >>>>>>>>> message
> > >>>>>>>>> like this:
> > >>>>>>>>>
> > >>>>>>>>> step -1: Water molecule starting at atom 16281 can not be
> > settled.
> > >>>>>>>>>
> > >>>>>>>>> It is for couple of water molecules. I have checked visually
> > where
> > >>>>>>>>> these
> > >>>>>>>>> molecules are and for minimization they are near surface of
> > protein
> > >>>>>>>>> (not
> > >>>>>>>>> buried inside). I attach the link for *gro, *top, *log and
> other
> > >>>>>>>>> files.
> > >>>>>>>>> What can I do about it?
> > >>>>>>>>>
> > >>>>>>>>> http://www.speedyshare.com/rN4gx/mCherry7-min.tar.bz2
> > >>>>>>>>> http://www.speedyshare.com/BnwU5/mCherry7-nvt-md.tar.bz2
> > >>>>>>>>> http://www.speedyshare.com/3k9jz/charmm27-files.tar.bz2
> > >>>>>>>>>
> > >>>>>>>>> Best wishes,
> > >>>>>>>>>
> > >>>>>>>>> Dawid Grabarek
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>    --
> > >>>>>>>>>
> > >>>>>>>>>  ==================================================
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>> Justin A. Lemkul, Ph.D.
> > >>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>>>>>>
> > >>>>>>> Department of Pharmaceutical Sciences
> > >>>>>>> School of Pharmacy
> > >>>>>>> Health Sciences Facility II, Room 601
> > >>>>>>> University of Maryland, Baltimore
> > >>>>>>> 20 Penn St.
> > >>>>>>> Baltimore, MD 21201
> > >>>>>>>
> > >>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > >>>>>>> http://mackerell.umaryland.edu/~jalemkul
> > >>>>>>>
> > >>>>>>> ==================================================
> > >>>>>>> --
> > >>>>>>> Gromacs Users mailing list
> > >>>>>>>
> > >>>>>>> * Please search the archive at http://www.gromacs.org/
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> > >>>>>>>
> > >>>>>>>
> > >>>>>>>   --
> > >>>>>>>
> > >>>>>> ==================================================
> > >>>>>
> > >>>>> Justin A. Lemkul, Ph.D.
> > >>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>>>>
> > >>>>> Department of Pharmaceutical Sciences
> > >>>>> School of Pharmacy
> > >>>>> Health Sciences Facility II, Room 601
> > >>>>> University of Maryland, Baltimore
> > >>>>> 20 Penn St.
> > >>>>> Baltimore, MD 21201
> > >>>>>
> > >>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > >>>>> http://mackerell.umaryland.edu/~jalemkul
> > >>>>>
> > >>>>> ==================================================
> > >>>>> --
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> > >>>>>
> > >>>>>
> > >>>>>  --
> > >>> ==================================================
> > >>>
> > >>> Justin A. Lemkul, Ph.D.
> > >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>>
> > >>> Department of Pharmaceutical Sciences
> > >>> School of Pharmacy
> > >>> Health Sciences Facility II, Room 601
> > >>> University of Maryland, Baltimore
> > >>> 20 Penn St.
> > >>> Baltimore, MD 21201
> > >>>
> > >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > >>> http://mackerell.umaryland.edu/~jalemkul
> > >>>
> > >>> ==================================================
> > >>> --
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> > >>>
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
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