On Fri, Apr 1, 2016 at 7:24 AM, Luke Presson <luke.presson.centre.edu> wrote:
>
> I have been doing research modeling inhibitors of enzymes and have recently run into a problem in which the ligand immediately breaks apart once the simulation starts.
This sounds like a problem with your parameters. How did you generate
parameters for this ligand?
> When I have visualized the simulation it appears as though the atoms in the ligand move independently but somehow maintain bonds even if they are over 10 angstroms apart.
Bond are never broken in a traditional MD simulation, so as long as
there is a bond defined in your topology that bond will appear in your
visualization program no matter how far apart the atoms in the bond
get.
-Dan
> This seems to be a more recent issue that I did not have while doing this research in the past. I have been using periodic boundaries and heating using NVT, then equilibrating with NPT. The one thing that I have found that works is if I turn off periodic boundaries, however I would like to be able to keep the system at constant pressure. I have not seen any previous posts of this problem happening and am wondering if anyone has some suggestions.
>
> Thanks,
> Luke Presson
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Fri Apr 01 2016 - 11:00:02 PDT
