[gmx-users] R: help with neighborsearching error
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 17 19:06:04 CET 2009
Anna Marabotti wrote:
> Dear Justin,
> I would like to say that now all things work...but it isn't!
> I tried to minimize my system with emtol 500 and emstep 0.1, then 0.5, then with emtol 1000 and emstep 0.5 and
> 1, but this time I did not arrive to convergence. It seems to me that every time I use this system, it
> "behaves" differently from the previous ones! I'm really sure to make the steps in the same way, since I
Well, you may not get identical results every single time you do something.
Your emstep values are a bit large, try something more like the default, 0.01;
otherwise you can try other minimizers, like CG, instead of SD.
> simply scroll the commands with the arrows and re-submit them! This time, I didn't noticed a difference in the
> number of water molecules after genbox: I re-tried a couple of times the entire procedure, but all was going
> wrong in the same way...
> Despite this, I tried to send a PR-MD with the suggested correction on PME (I simply added "coulombtype = PME"
> in the pr.mdp file) and this is the error message I found (at least, it is different from previous ones...):
>
Bad idea, if the minimization didn't converge.
-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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