[gmx-users] R: help with neighborsearching error
Anna Marabotti
anna.marabotti at isa.cnr.it
Tue Feb 17 18:12:01 CET 2009
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
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...):
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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