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: amarabo...@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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
