[gmx-users] Adding buffer to simulation box

Mark Abraham mark.j.abraham at gmail.com
Tue May 2 17:27:32 CEST 2017


Everything that goes into your simulation cell has to have a topology file,
so you'll need to develop one for citrate anion. And then do the simple
arithmetic to work out how many of each species you need in your cell to be
a model of your conditions of interest.


On Tue, May 2, 2017 at 4:53 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>

> Hi all,
> I want to run an MD simulation in presence of 20mM Sodium Citrate buffer
> at pH4.5 . How would I go about adding this buffer to the simulation box? I
> have tried adding it in the same way as counter-ions but it did not work. I
> am aware of the gmx insert molecules command but I'm not sure whether I
> need a buffer topology file for this?
> Akash
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