Re: [gmx-users] Adding buffer to simulation box

t; Abraham > Sent: 02 May 2017 16:27 > To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Adding buffer to simulation box > > Hi, > > Everything that goes into your simulation cell has to have a topology > file, so you'll nee

Re: [gmx-users] Adding buffer to simulation box

...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 02 May 2017 16:27 To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Adding buffer to simulation box Hi, Everything that goes into your simulation

Re: [gmx-users] Adding buffer to simulation box

Hi, 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. Mark On Tue, May 2, 2017 at

[gmx-users] Adding buffer to simulation box

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