[gmx-users] Water molecule can not be settled - mdrun error
jalemkul at vt.edu
Fri Sep 21 16:04:20 CEST 2012
On 9/21/12 9:45 AM, Lara Bunte wrote:
> 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
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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