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 :)) -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
