[gmx-users] Adding buffer to simulation box

[Mark Abraham]

Hi,

Extensibility, and availability of quality automated tool support for that
are things that should go into your choice of force field. There may be
such for OPLS (I literally don't know). You need to choose an appropriate
force field; that means you need one that has citrate, or can be extended
with an appropriate amount of effort to do a good job of modelling it.

Mark

On Fri, May 5, 2017 at 12:26 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> I'm using the OPLS ff but I can't seem to find a tool in which I can
> generate topology for this force field. I looked up the ones recommended on
> GROMACS but had no luck. I also have SWISSParam but that is for CHARMM.
>
> Akash
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 02 May 2017 16:27
> To: gmx-users at gromacs.org; gromacs.org_gmx-users at 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 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 4:53 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
> wrote:
>
> > 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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