[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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