On Tue, Jul 21, 2015, Sharapa wrote:
>
> I want to make MD on a small organic molecule containing Si.
> (trialkylsilyl group)
> I thought on usage GAFF, but there is no parameters for Silicon.
> I found http://archive.ambermd.org/200804/0353.html, but i am badly
> confused that as far as i understand parameters simply copied from
> carbon. That looks little bit weird for me.
>
> I tried to generate parameters by my own
> 1) bond length and angles from DFT and MP2 calculations
> 2) force constants by parmgen. Seems this way they depends only on a
> bond length and not on a type of atom, that isn't true generally for
> gaff.dat, but ok, they looks not too strange so i accept them.
> 3) wdv-radii and 6/12 parameter that i found in papers fits to mentioned
> on a link (Si 2.220 0.320) and seems i can ignore polarisation.
> (I put my parameters at the end of the email)
These look OK for a start. Of course, you should do some simple simulations,
say of the Si-containing molecule by itself to see what problems exist.
> Nevetherless i have problem with dihedrals.
Most torsion terms should be small, and probably not that much different from
the corresponding carbon terms.
> I tried to follow
> http://www.ub.edu/cbdd/?q=content/small-molecule-dihedrals-parametrization
> and perform set of Gaussian MP4//MP2 calculations but didn't succed even
> with tetramethylsilane molecule (multiple unclear problems with
> run_all_sander_param.sh script).
This is not a good way to get help: saying you have "multiple unclear
problems" is not specific enough.
> I tried to search answer on
> http://q4md-forcefieldtools.org/REDServer-Development/ but the part i
> liked the most FFParmDev seems does not exist.
Again, we (or Francois) would need more specific information. It's easy for
pages on a web page to become stale or unavailable. You can help by giving
detail info on what you tried and what the error was.
....good luck....dac
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Received on Tue Jul 21 2015 - 06:00:04 PDT
