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

Mark Abraham mark.j.abraham at gmail.com
Mon Aug 11 22:56:49 CEST 2014 

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/
> >>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>>>>
> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>>>
> >>>>>>> * For (un)subscribe requests visit
> >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >>>>>>> or
> >>>>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>>>
> >>>>>>>
> >>>>>>>   --
> >>>>>>>
> >>>>>> ==================================================
> >>>>>
> >>>>> 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/
> >>>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>>
> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>
> >>>>> * For (un)subscribe requests visit
> >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>
> >>>>>
> >>>>>  --
> >>> ==================================================
> >>>
> >>> 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/
> >>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>>
> > --
> > ==================================================
> >
> > 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/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list