[gmx-users] error in starting/completing minimization

Rashek Kazi rashek.kazi at gmail.com
Mon Apr 23 23:38:43 CEST 2012

Dear all,

I am trying to conduct some simple ligand binding studies for a protein
system solvated in water. After inputting the command:

mdrun -v -deffnm em -nt 1

I get the log shown below, nothing completes after this 0 step. Any help
would be appreciated.

Back Off! I just backed up em.log to ./#em.log.14#
Getting Loaded...
Reading file em.tpr, VERSION 4.5.4 (single precision)
Loaded with Money

Back Off! I just backed up em.trr to ./#em.trr.3#

Back Off! I just backed up em.edr to ./#em.edr.3#

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Warning: 1-4 interaction between 1 and 8 at distance 4.764 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
mdrun -v -deffnm em -nt[1]+  Segmentation fault: 11  mdrun -v -deffnm em
-nt 1
104-142:GLY lwollmuth$ tail -15 em.log
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.

Removing pbc first time

S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

The mdp input file is as below:

title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep       = 0.01       ; Energy step size
nsteps = 50000   ; Maximum number of (minimization) steps to perform
energygrps = Protein   ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1    ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)

Rashek Kazi
GS 2
MSTP Candidate
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