[gmx-users] Failed Energy Minimization

[Justin M. Shorb]

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 (gmx-users at gromacs.org)
-------------------------------------------------------

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				shorb at wisc.edu
University of Wisconsin-Madison,  Department of Chemistry
1101 University Ave., Madison, WI, 53706