Hello Marcelo,
> I´m trying to perform some simulations in different organic solvents,
> such as acetonitrile and DMSO.
> Is there any database of organic solvents for using in MD simulations?
You will find many examples of organic solvents in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/
i.e. not only acetonitrile & DMSO. More will come:
http://q4md-forcefieldtools.org/REDDB/uploadfile/W-80/
You can use the "Download project" tool to perform a search using
"Molecule keyword" (Molecule keyword = Solvent; Molecule keyword =
Sulfoxide; Molecule keyword = Nitrile). You can use "Molecule name =
dimethylsulfoxide" or "Molecule name = acetonitrile" as well.
You will find also a new seach tool "Theory level/Basis set".
See for instance:
http://q4md-forcefieldtools.org/REDDB/up/W-1/
...
http://q4md-forcefieldtools.org/REDDB/up/W-46/
up to
http://q4md-forcefieldtools.org/REDDB/up/W-49/
For a solvent, you will find different force field libraries depending
on the procedure used to derive the atomic charges. If you get lost
between the similar projects available in R.E.DD.B. for a same
solvent, read the Abstract (Project summary) and look at the Keywords
used during the charge deviation.
In each R.E.DD.B. project, a force field library is in the Tripos mol2
file format, which can be directly used in LEaP (sleap, tleap,
xleap...) or VMD...
You can use the LEaP script available in a project to load the
selected force field library in LEaP as provided in:
http://q4md-forcefieldtools.org/REDDB/up/W-46/script1.ff
I hope this helps,
regards, Francois
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Received on Fri Dec 05 2008 - 14:49:09 PST
