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

Justin Lemkul jalemkul at vt.edu
Mon Aug 11 15:03:34 CEST 2014 


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
>>>>
>>>> ==================================================
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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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-- 
==================================================

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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