On 26/01/2012 5:10 PM, Alex Seling wrote:
Hello,
After upgrading to gromacs 4.5.5, the old .mdp file that was working
is now giving me errors.
Marginally stable numerical integration can work out, or not. Here, you
are using a time step that is not suitable for a simulation lacking bond
constraints. See section 6.5 of manual, for example. If you really want
infinite cut-offs, read 7.3.9. Normal practice to avoid problems is to
use an equilibration regime whose integration scheme is more gentle than
your simulation regime.
Mark
Specifically, I'm getting
"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.
This is with a good starting configuration. Any ideas as to the error?
My .mdp file is below.
Thanks,
Alex Seling
title = lea at 300K
cpp = /lib/cpp -traditional
integrator = md ;sd ;md ;bd
tinit = 0.0
dt = 0.001 ;time step of 1 fs
nsteps = 238000000 ;1 us @ 1fs
nstxout = 200000 ; frequency to write coordinates to output trajectory
file = 1ns
nstxtcout = 200000 ; frequency to write coordinates to xtc trajectory
= 1 ns
nstvout = 0
nstfout = 0
nstlog = 200000 ; frequency to write energies to log file = 1 ns
nstenergy = 200000 ; frequency to write energies to energy file = 1ns
energygrps = system
comm_mode = angular
nstcomm = 40
nstlist = 100
nstype = simple
pbc = no
rlist = 100
rgbradii = 100
coulombtype = cut-off
epsilon_r = 1 ; double check this is what we want
rcoulomb = 100
vdwtype = cut-off
rvdw = 100
tc-grps = system
tau_t = 0.01099
ref_t = 300
gen_vel = yes
gen_temp = 273
constraints = none
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78
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