[gmx-users] Re: help with neighborsearching error
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 17 16:32:32 CET 2009
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
> 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.
> Many many thanks and best regards
> 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
jalemkul[at]vt.edu | (540) 231-9080
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