[gmx-users] R: help with neighborsearching error
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 17 19:10:51 CET 2009
Justin A. Lemkul wrote:
> Bad idea, if the minimization didn't converge.
I should amend that: "Bad idea, if the minimization didn't converge to
reasonable values of Epot and Fmax."
-Justin
>
>> Step 502, time 1.004 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> max 25670116.000000 (between atoms 1615 and 1616) rms 674225.375000
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 168 169 89.9 0.1000 0.1254 0.1000
>> 171 172 37.0 0.1000 0.1013 0.1000
>> 171 173 89.9 0.1000 0.1157 0.1000
>> 174 175 89.9 0.1000 0.1299 0.1000
>> 174 176 60.8 0.1000 0.0995 0.1000
>> 1564 1565 34.6 0.1000 0.1001 0.1000
>> 1592 1594 39.6 0.1330 0.1831 0.1330
>> 1594 1595 43.8 0.1000 0.1448 0.1000
>> 1594 1596 111.2 0.1470 3329.0908 0.1470
>> 1596 1597 105.8 0.1530 3329.1094 0.1530
>> 1596 1603 105.5 0.1530 21318.4980 0.1530
>> 1597 1598 36.5 0.1530 0.1972 0.1530
>> 1600 1602 89.8 0.1000 0.2606 0.1000
>> 1603 1604 105.8 0.1230 21076.9980 0.1230
>> 1603 1605 102.2 0.1330 95833.0078 0.1330
>> 1605 1606 100.2 0.1000 87086.0078 0.1000
>> 1605 1607 93.6 0.1470 464589.8125 0.1470
>> 1607 1608 93.4 0.1530 464721.6250 0.1530
>> 1607 1615 95.8 0.1531 768441.6250 0.1530
>> 1608 1609 96.3 0.1530 109266.5625 0.1530
>> 1609 1610 96.6 0.1530 16824.1641 0.1530
>> 1610 1611 120.4 0.1230 2709.7004 0.1230
>> 1610 1612 114.4 0.1330 2709.6948 0.1330
>> 1612 1613 53.7 0.1000 0.1715 0.1000
>> 1612 1614 50.3 0.1000 0.1618 0.1000
>> 1615 1616 90.9 0.1250 3208764.5000 0.1250
>> 1615 1617 94.9 0.1250 802098.3125 0.1250
>>
>> Back Off! I just backed up step501.pdb to ./#step501.pdb.1#
>> Wrote pdb files with previous and current coordinates
>> [lilligrid:22985] *** Process received signal ***
>> [lilligrid:22985] Signal: Segmentation fault (11)
>> [lilligrid:22985] Signal code: Address not mapped (1)
>> [lilligrid:22985] Failing at address: 0x14b50070
>> [lilligrid:22985] [ 0] /lib64/libpthread.so.0 [0x381440de70]
>> [lilligrid:22985] [ 1] mdrun [0x56cd54]
>> [lilligrid:22985] *** End of error message ***
>>
>> When I repeated the procedure, the errors were not on the same atoms.
>> However, these deviations are on atoms
>> belonging to protein. On the contrary, on the .log files concerning
>> minimization there are errors again on
>> water molecules.
>> Anna
>>
>> -----Messaggio originale-----
>> Da: Justin A. Lemkul [mailto:jalemkul at vt.edu] Inviato: martedì 17
>> febbraio 2009 16.33
>> A: Anna Marabotti; Gromacs Users' List
>> Oggetto: Re: help with neighborsearching error
>>
>> Anna Marabotti wrote:
>>> Dear Justin,
>>> I hope you wouldn't mind if I contact you directly, but I think I
>>> cannot send you the requested .log file
>> via
>>> the gmx-users list because the message would be filtered.
>>
>> It is best to keep the discussion on the list; posting short .mdp
>> files (pasted into the text of the mail, not sent as attachments) will
>> not cause your messages to be filtered.
>>
>>> I'm attaching here the em.mdp file and the pr.mdp file I used for my
>>> simulations. For em.mdp, this is the
>>> "last" version, but I made changes on nsteps and emsteps as I
>>> described you previously. I also changed the
>>> emtol raising it down until 500: nothing worked. The only thing I
>>> never changed is the integrator. I never
>>> changed the parameters for PR-MD during all my attempts on this
>>> protein. On other proteins similar to this
>>> one, the file pr.mdp seems to work well.
>>>
>>
>> An emtol of 500 is reasonable (just checking).
>>
>>> About genbox problem, I noticed that a couple of times the number of
>>> water molecules changed even if the box
>>> shape was the same as previously (BTW, the distance I reported is the
>>> one between solute and box edge (i.e.,
>>> editconf -d). However, things don't work even when the number of
>>> water molecules is the same.
>>>
>>
>> I still don't understand why this would be happening, but it is
>> probably not your problem (see below).
>>
>>> I forgot to tell that the protein I'm using is a monomeric protein
>>> that I obtained deleting a chain from the
>>> PDB file, in which it appears as a dimer in the crystallographic cell
>>> (a procedure that I applied several
>>> other times without problems). The monomers are not in contact in the
>>> PDB file. I tested both monomers, and
>>> both of them experiment errors.
>>>
>>> Lastly, the GROMACS I'm using is installed in single precision, so I
>>> cannot use the double precision for
>>> minimization.
>>>
>>> I'm almost certain that the problem is a stupid thing that I cannot
>>> see, but it's almost a week that I'm
>>> checking this system and now I'm exhausted! I hope the Murphy's law
>>> on errors will work this time. Please
>>> forgive me!
>>
>> From your pr.mdp file:
>>
>> title = position-restrained dynamics
>> cpp = /usr/bin/cpp
>> define = -DPOSRES
>> constraints = all-bonds
>> integrator = md
>> dt = 0.002 ; ps !
>> nsteps = 10000 ; total 20 ps.
>> nstcomm = 1
>> nstxout = 500
>> nstvout = 500
>> nstfout = 500
>> nstlog = 500
>> nstenergy = 500
>> nstlist = 500
>> ns_type = grid
>> rlist = 0.9
>> rcoulomb = 0.9
>> rvdw = 1.4
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl = berendsen
>> tc-grps = Protein Non-Protein
>> tau_t = 0.1 0.1
>> ref_t = 300 300
>> ; Energy monitoring
>> energygrps = Protein Non-Protein
>> ; Pressure coupling is not on
>> Pcoupl = no
>> tau_p = 0.5
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel = yes
>> gen_temp = 300.0 300.0
>> gen_seed = 173529
>>
>> You have not specified coulombtype, therefore you are using the
>> default of "cut-off." You are probably going to see artefacts of such
>> a setup, which may lead to incorrect behavior; use PME.
>>
>> -Justin
>>
>>> Many many thanks and best regards
>>> Anna
>>> ______________________________________________
>>> Anna Marabotti, Ph.D.
>>> Laboratory of Bioinformatics and Computational Biology
>>> Institute of Food Science, CNR
>>> Via Roma 64
>>> 83100 Avellino (Italy)
>>> Phone: +39 0825 299651
>>> Fax: +39 0825 781585
>>> Skype: annam1972
>>> E-mail: amarabotti at isa.cnr.it
>>> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
>>> ____________________________________________________
>>> "If you think you are too small to make a difference, try sleeping
>>> with a mosquito"
>>
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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