On 2/02/2012 3:36 PM, Alex Seling wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
"This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size"
for a few interactions, with each of them approaching inf.
The usual advice and diagnostic procedure can be found here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Can anyone find anything glaringly wrong with my .mdp?
No constraints often requires a time step of 0.0005ps.
Mark
Thanks,
Alex Seling
title = Minimization of alpha-synuclein
cpp = /lib/cpp -traditional
define = -DFLEXIBLE
integrator = sd
constraints = none
tinit = 0
dt = 0.001
nsteps = 1000000
emtol = 0.00001
emstep = 0.1
nstcgsteep = 1000
bd-fric = 0
nstlog = 50
nstenergy = 1
gen_temp = 273
gb_epsilon_solvent = 78.3
implicit_solvent = GBSA
gb_algorithm = Still
nstcomm = 10
xtc_precision = 1000
gen_vel = yes
nstxtcout = 0
nstxout = 100
pbc = no
energygrps = system
nstfout = 0
nstvout = 0
niter = 20
nstlist = 10
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