[gmx-users] problem with energy minimization

sanjay23 at iitb.ac.in sanjay23 at iitb.ac.in
Mon May 12 12:39:02 CEST 2008


Dear gromacs user,
I am doing simulation of Gal1P protein in explicit solvent.when i did
energy minimization of system i got this warning:-
Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 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
if not, you should increase table-extension in your mdp file.

i added table -extention 1.1 in mdp file but i am steel gettingsame
problem.kindly help me.
i am pasting em.mdp file for your considerartion
thanks in advance.
title               =   Gal1p
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
dt                  =  0.002    ; ps !
nsteps              =  50000
nstlist             =  10
nstcomm             =  1
nstxout             =  1000
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.1
;
;       Energy minimizing stuff
;
emtol               =  100
emstep              =  0.01





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