[gmx-users] Deuterate organic solvent
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.
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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