Hi Justin, thank you for quick reply. You are right I have practicle result, And I want to replicate them..
Thank you for your suggestion.. With Best Wishes, Rama David On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > 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 <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 EM? > > 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. >
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