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i m carryin a protein explicit solvent simulation using gromacs 3.3 <br>
for intially minimizing the hydrogen i did some small mini and equi in the vaccum by maintaing the restraints <br>
then i added ions and water but in the very first minimization i m getting the following error <br>
<br>
<br>
1-4 interaction between 1 and 9 at distance 8.454 which is larger than the 1-4 table size 1.000 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
<br>
<br>
in the log file im geting :<br>
<br>
4 inconsistant shifts check ur topology <br>
<br>
following is my input file :<br>
<br>
title = 1min in water<br>
define = -DPOSRES<br>
integrator = steep<br>
dt = 0.001<br>
constraints = none<br>
nsteps = 500<br>
nstlist = 10<br>
rcoulomb = 1<br>
rlist = 1<br>
rvdw = 1.4<br>
ns_type = grid<br>
coulombtype = PME<br>
pbc = xyz<br>
gen_vel = no<br>
fourierspacing = 0.12<br>
pme_order = 6<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
comm_mode = angular<br>
emtol = 100.0<br>
emstep = 0.01<br>
<br>
<br>
after adding the ions i have modified the topology file, <br>
plz tel me what is the exact reason for this error or what are
the other things i should check in relation to the error <br>
<br>
<br>
thanks <br>
<br>
<br>
Gurpreet<br>
IIT MADRAS <br>
<br>