From: Nathan Kern (
Date: Sat Nov 20 2021 - 13:16:21 CST

Dear Francesco,

I am not sure how to do it in VMD, but this is a good use case for
CHARMM-GUI Multicomponent Assembler <;!!DZ3fjg!rKrsb7DS3vI2LV124N6NukkSQ2Ktum5p9-GkaMuq3H_I95vU2ukbS8o-yEse6n8CMQ$ >.
This <;!!DZ3fjg!rKrsb7DS3vI2LV124N6NukkSQ2Ktum5p9-GkaMuq3H_I95vU2ukbS8o-yEufffxUZg$ > demo should be similar
to what you are trying to achieve.


On Sat, Nov 20, 2021, 11:04 AM Francesco Pietra <>

> Hello
> I am trying to carry out MD with a mono-positively charged organic
> molecule (small molecule, "natural product") in chloroform.
> It seems to me that there is no point - or no easy way - to neutralize.
> That mono-positively chrged molecule (NMR identified) represents one of the
> species in a complex environment containing the MsOH strong acid, and where
> the prevalent existing base is also an organic molecule
> thanks for advice
> francesco pietra