[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
> 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.


> 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


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