You will not have an extra time with this if you want your simulation to go
a long time. For starters you can use the AddToBox utility in amber/bin
(run with no arguments to see the list of things you can do). That will
help you randomly mix acetonitrile and water initially (make sure to
minimize before starting dynamics).
But if you simulate just a few hundred acetonitriles and a thousand waters
(or whatever the ratio needs to be), then check after 50ns or so, and find
that they separate (which appears likely) you have as DAC said an imbalance
in your FF and a parameter development problem.
Once you get your solvents to stay mixed, round II: protein in solvent
mixture. You could very well find that the protein gets coated in
acetonitrile and that the acetonitrile gets leached out of solution in the
process. To determine whether THAT is realistic or not you will need the
right kind of experimental data.
Dave
On Apr 5, 2017 10:48 AM, "Sowmya Indrakumar" <soemya.kemi.dtu.dk> wrote:
> Hi Andreas,
> I am not sure if this is feasible.
> Since you already know the ratio, you can do the following
> 1.solvate you protein
> 2.replace some of the water with the other molecule. For instance,
> *addions* randomly replaces water with the ion you give.
> Regards
> Sowmya
> ________________________________________
> From: David A Case [david.case.rutgers.edu]
> Sent: Wednesday, April 05, 2017 4:37 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Acetonitrile Water Mix
>
> On Wed, Apr 05, 2017, Andreas Tosstorff wrote:
> >
> > I am trying to simulate a protein in a 60% acetonitrile, 40% water
> mixture.
> > I observed that the two solvents arrange in layers rather than to form a
> > homogeneous mix. See the attached pictures and input files.
> > Any advice on how to perform simulations with solvent mixtures?
>
> Sounds like you already know how to perform the simulations. If these two
> liquids are supposed to be miscible, then there is likely an inbalance in
> your
> force field. Try a Google search on something like "acetonitrile water
> force
> field" to see what others have done in simulating this sort of mixture.
>
> ....dac
>
>
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Received on Wed Apr 05 2017 - 08:30:02 PDT
