[gmx-users] Water molecule can not be settled - mdrun error

Lara Bunte lara.bunte at yahoo.de
Fri Sep 21 17:26:16 CEST 2012

Hi Justin

Sorry but I don't understand what you mean with "Despite being given the correct settings for CHARMM27, you're still not using 
them." I use exactly the settings Peter gave me in my last question. What is in this settings wrong and where could I find the right settings?


----- Ursprüngliche Message -----
Von: Justin Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 16:04 Freitag, 21.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error

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 

> 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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