[gmx-users] Deuterate organic solvent

Jonathan Saboury jsabou1 at gmail.com
Sun Sep 29 07:24:51 CEST 2013

I want to run a simulation of cyclohexane in deuterated chloroform.

I was able to run a sim of cyclohexane in regular chloroform, but unable to
find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh
and -deuterate option, would I do it this way? It isn't a protein and would
assume I would get an error.

I know these sims are based off of newton's laws of motion, and that is
pretty much where my understanding stops. I assume that the hydrogen’s have
a mass of ~1, and that I need to change them to ~2.

I look at the .itp's generated by acpype and all the masses are set to 0
(is this alright?) Note: all [atomtypes] are in cyclohexane_GMX.itp.

Another problem I see happening that the atomtypes are all sharing the same
atomtype, so possibly any sp3 C-H bond is going to be deuterated since they
all share the same definition.

commands: http://pastebin.com/raw.php?i=jGZV8k2t
cyclohexane_GMX.itp: http://pastebin.com/raw.php?i=Q6MrURmN
chloroform_GMX.itp: http://pastebin.com/raw.php?i=pAHaUSVv

Entire folder download: http://www.sendspace.com/file/frc1uy

Is there an automatic way to have a specific solvent be deuterated?

Thank you for the help :))

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