Justin, Your email makes me wonder two things.
1. Are you doing a series of energy minimizations? Do you start with an
emtol of say 50000, then depending on the results of that, reduce it to
25000 and so on until you reach the recommended value of 100?
It is unclear when you say
If I try running with ns_type = simple, the em runs until it
hits around 35
whether you mean energy minimization is at 35 steps in one cycle at a
particular tolerance, or is 35 the tolerance at which it fails or I don't
know...
2. Have you tried an energy minimization cycle with only your peptide9s(s)
and no water at all?
I hope this is helpful, Jennifer
-------------------------------------------------------------------------------
Jennifer Rendell
Department of Biochemistry
Memorial University of Newfoundland
St. John's, Newfoundland
CANADA A1B 3X9
-------------------------------------------------------------------------------
Message: 2
Date: Thu, 19 Apr 2007 18:01:05 -0500
From: "Justin M. Shorb" <[EMAIL PROTECTED]>
Subject: [gmx-users] Failed Energy Minimization
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Greetings:
I have been having trouble running any energy minimization with any
sort of system. I have small polypeptides in water, and then large
proteins in water with the same error message:
Steepest Descents:
Tolerance (Fmax) = 2.00000e+02
Number of steps = 10000
Step= 0, Dmax= 2.0e-02 nm, Epot= -2.84070e+04 Fmax= inf,
atom= 17
-------------------------------------------------------
Program mdrun_d, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or
parameter
errors that give particles very high velocities you might end up with
some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the
potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 ..
125 ]
Please report this to the mailing list ([email protected])
-------------------------------------------------------
No matter what run parameters I get, I always get ci = -2147483648.
Even different systems. (This, I realize is simply numerically
infinity). If I try running with ns_type = simple, the em runs until it
hits around 35 and then says it didn't converge. Since I am running
grompp_d -v, I get that there are certain atoms that have infinite
potential. But, depending on the system, the atom type (solvent or
molecule) changes.
I have noted that previous posts have been answered with an admonition:
"Find out which atoms are infinite force, and then fix it." I suppose I
could go through, find the atoms and remove those waters that overlap,
but shouldn't this be taken into account by the genbox_d program? I
also have tried to increase the vdw radii in the vdwradii.dat file to
have it delete more waters. But, even after having 60 fewer waters
around a 88 kD protein, the system still fails to energy minimize.
Given that this seems to be a common problem in solvating a system, are
there better options (options for genbox??) than running the following
shell commands? The em.mdp file is also shown below.
Thanks for your help,
Justin
# Set up the files
# First, the pdb is generated into a gro file, and other files
pdb2gmx_d -f ${INPUTPDB} -o ${MOL}.gro -i posre.itp -p ${MOL}_spc.top
-ter < p2g.in
# Now modify the .pdb to use a periodic box
editconf_d -bt cubic -f ${MOL}.gro -o ${MOL}.gro -c -d ${PBCx}
#Solvate the box with spc, but the water type can be changed in next
line
genbox_d -cp ${MOL}.gro -cs spc216.gro -o ${MOL}-sol_b4em.gro -p
${MOL}_spc.top
# Now we specify which topology to use for our water (by default, SPC)
sed -e ${WATER} ${MOL}_spc.top >> ${MOL}-sol.top
# Now everything is solvated, so we switch molecular names (for
simplicity)
MOL="${MOL}-sol"
# Perform Energy Minimization (necessary when solvating)
# GROmacs Pre-Processor
grompp_d -v -f em.mdp -c ${MOL}_b4em.gro -p ${MOL}.top -o ${MOL}_em
mdrun_d -v -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4eq
# Perform equilibration of the system
grompp_d -f eq.mdp -c ${MOL}_b4eq.gro -p ${MOL}.top -o ${MOL}_eq
mdrun_d -s ${MOL}_eq -o ${MOL}_eq -c ${MOL}_b4md
# Perform MD
grompp_d -f md.mdp -c ${MOL}_b4md.gro -p ${MOL}-v.top -o ${MOL}_md
mdrun_d -s ${MOL}_md -o ${MOL}_md -c ${MOL}_final
CUT=1.20
#------- Energy Minimization: em.mdp -------#
cat > em.mdp <<EOF
title = ${MOL}
cpp = /usr/bin/cpp
define = -DFLEX
constraints = none
integrator = steep
nstlog = 100
ns_type = grid
dt = 0.001 ; ps !
nsteps = 10000
nstlist = 1
coulombtype = PME
rlist = ${CUT}
rcoulomb = ${CUT}
rvdw = ${CUT}
pme_order = 6
fourierspacing = 0.05
ewald_rtol = 1e-5
;
; Energy minimizing stuff
;
emstep = 0.02
emtol = 200.0
EOF
_________________________________________________________________
Justin M. Shorb Phone: (608) 262-0483
Skinner Group [EMAIL PROTECTED]
University of Wisconsin-Madison, Department of Chemistry
1101 University Ave., Madison, WI, 53706
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