[gmx-users] Re: gmx-users Digest, Vol 59, Issue 58

[Andrew Voronkov]

I've used this tutorial:
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf 
 
I've used command line:  editconf -c -f conf.gro -bt dodecahedron -d 0.7 -o box.gro to center the protein, but the problem remains - protein is still in the edge of the water box.

There is also 1-4 warning for which I see no reasons and very fast presision reached time.

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =          200
Warning: 1-4 interaction between 2 and 21 at distance 6.197 which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step=   14, Dmax= 1.2e-06 nm, Epot=  2.82932e+24 Fmax=         inf, atom= 4
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  =  2.8293175e+24
Maximum force     =            inf on atom 4
Norm of force     =            inf

gcq#239: "killing children ..." (Insight/Parasoft)

andrew at linux-f29d:~/GROMACS_MD/FZD1> 

Here are MDP files:

EM.mdp
integrator = steep
nsteps = 200
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
nstenergy = 10
constraints = none


integrator = md
nsteps = 2500
dt = 0.002
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
tcoupl = Berendsen
tc-grps = protein non-protein
tau-t = 0.1 0.1
ref-t = 298 298
Pcoupl = Berendsen
tau-p = 1.0
compressibility = 5e-5 5e-5 5e-5 0 0 0
ref-p = 1.0
nstenergy = 100
define = -DPOSRES

Best regards,
Andrew
> ------------------------------
> Message: 3
> Date: Fri, 06 Mar 2009 13:41:28 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] .gro files problems
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49B16E58.3000401 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Andrew Voronkov wrote:
> > Dear GROMACS users,
> > I'm trying to do this tutorial
> > 
> It's always best to post a link to the tutorial you're using.  There are dozens 
> of Gromacs tutorials out there.
> > with 1ijy structure from rcsb.org
> > All .gro files on different step raise questions.
> > 1) conf.gro - by VMD I see some strange groups which are not linked with the protein.
> This may or may not be an artefact of VMD's efforts to guess where bonds should 
> be.  Sometimes it's smart, sometimes it's not.
> > 2) After solvatation step in solvated.gro the protein is not in the middle of solution but somewhere in the edge, how to solve this?
> editconf -c
> > 3) After energy minimization protein even goes out of the solution. Looks like I am doing everything according to the tutorial (except the structure) but there are still problems...
> > 
> Use editconf -c and try again.
> > The .gro files are in the attachment.
> The listserv ate them, but they probably won't aid much in diagnosis, anyway.
> > On minimization step I also get:
> > Steepest Descents converged to machine precision in 73 steps,
> > but did not reach the requested Fmax
> Depending on what your target Fmax was, this may not be a problem.  Fmax < 1000 
> is generally adequate for a simple protein in water.
> > On equilibration step I also get an error(with such .gro file it very proabable):
> > 
> Or you could have an error in your .mdp file (inappropriate parameters, etc), so 
> if things continue to fail, post the .mdp file (not as an attachment, just embed 
> the text).
> -Justin