[gmx-users] LINCS warnings
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 11 12:28:00 CEST 2012
On 6/11/12 6:23 AM, rama david wrote:
> Hi Mark,
> I did simulation of the same system in vacuum, and system behave the normally,
> So the instability in the system is due to the spc Water model???
> As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up
The water model is not the problem. Your solvated system has clashes that cause
instability. In vacuo, your solute has greater freedom to shift around.
> I think the source is (Please tell me is it right..?? or any else reason )
> last option :
> you have a single water molecule somewhere within the system that is isolated
> from the other water molecules.
> How to find such water molecule and solve the problem??
I think this is unlikely. If you have any isolated waters, they might be
sandwiched somewhere in your protein layers and should be easy to spot. The
best strategy is to use the output of EM to your advantage. Look at the atom
that had the highest force on it. What is it near? What might it be clashing
with? What if you run EM in vacuo, followed by solvation, and another round of
From your earlier description, it seems to me that the system has been
constructed to replicate some known experimental spacing, but doing so does not
guarantee that whatever peptide structure you are replicating will necessarily
produce a sensible result, or one that is free from clashes. Hence, you need to
refine the model before continuing.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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