[gmx-users] Water molecule near protein surface cannot be settled.
Dawid das
addiw7 at googlemail.com
Mon Aug 11 15:01:10 CEST 2014
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.
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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