On 9/21/12 9:45 AM, Lara Bunte wrote:
Hello
My equilibration of water around lumiflavin works (I got no error, no warning
and no note). Sadly the mdrun fails with following error:
step 886: Water molecule starting at atom 7596 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
What does GROMACS mean with "check bad contacts" and what do you think I should
fix?
"Bad contacts" refer to atomic clashes that arise either due to insufficient
minimization or broken model physics that cause molecules to collide with one
another.
System is lumiflavin in water, CHARMM 27 force field, tip3p water model.
Here is my mdp file I used before:
define = -DPOSRES
integrator = md
dt = 0.002
emtol = 1000.0
emstep = 0.01
nsteps = 5000
nstlist = 1
rlist = 1.2
rlistlong = 1.4
rcoulomb = 1.2
coulombtype = pme
vdw-type = cut-off
rvdw = 1.2
Despite being given the correct settings for CHARMM27, you're still not using
them. It makes it hard to help when you ignore what you've been told.
The other option, of course, is that the topology is not sound. How did you
derive the parameters for lumiflavin? Have you validated them in any way? Does
a simulation of lumiflavin in vacuo succeed?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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