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

Dawid das addiw7 at googlemail.com
Mon Aug 11 15:24:35 CEST 2014 

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
>>>>>>>
>>>>>>> ==================================================
>>>>>>> --
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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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
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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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> Gromacs Users mailing list
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