On 4/23/12 5:38 PM, Rashek Kazi wrote:
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,
Please see:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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