[gmx-users] Re: error during the minimization

[M.N. Manoj]

It could be an error in protein structure ( because 1 - 9 interaction ), and
we usually overcome similar issues by a pre -energy minimization before
submitting to gromacs.

i m carryin a protein explicit solvent simulation  using gromacs  3.3
for intially minimizing the hydrogen i did some small mini and equi in the
vaccum by maintaing the restraints
then i added ions and water but in the very first minimization i m getting
the following error


1-4 interaction between 1 and 9 at distance 8.454 which is larger than the
1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,


in the log file im geting :

4 inconsistant shifts check ur topology

following is my input file :

title               = 1min in water
define              = -DPOSRES
integrator          = steep
dt                  = 0.001
constraints         = none
nsteps              = 500
nstlist             = 10
rcoulomb            = 1
rlist               = 1
rvdw                = 1.4
ns_type             = grid
coulombtype         = PME
pbc                 = xyz
gen_vel             = no
fourierspacing      = 0.12
pme_order           = 6
ewald_rtol          = 1e-5
optimize_fft        = yes
comm_mode           = angular
emtol               = 100.0
emstep              = 0.01


after adding the ions i have modified the topology file,
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


thanks


Gurpreet
IIT MADRAS

-- 
M.N. MANOJ
PROJECT LEADER - BIOINFORMATICS
VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION
BANGALORE
INDIA
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