[gmx-users] Place water away from existing atoms
s.neumann08 at gmail.com
Thu May 17 17:16:22 CEST 2012
Thank you. Is it possible that this is caused by the trapped molecules
inside my tube? My tube ends are on the box edges so water cannot migrate
outside the tube where are the other water molecules.
On Thu, May 17, 2012 at 3:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> On 5/17/12 10:38 AM, Steven Neumann wrote:
>> Well, I am still getting the same error when I try to do minimization:
>> molecule on atom X cannot be settled" - these water molecules are not
>> close to
>> the Tube surface. If I will remove them the same error will occur but on
>> other atoms. If I specified only vdwradii for my Tube atoms why in the
>> bulk of
>> water there are some overlaps? Can you please help?
> The problem is not necessarily with the water molecule, but is more often
> indicative of some other instability in the system, such that forces are
> transmitted to that poor unsuspecting water molecule and it blows up.
> It's hard to diagnose, so make sure you're EM step is very small and you
> save configurations frequently in order to diagnose what's happening. It
> could be a problem with the .mdp file, topology, or perhaps some weird
> water overlap, but if that's the case, then genbox didn't do it, something
> else caused it.
> 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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