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--- Marcos S.A. On Wed, Apr 5, 2017 at 12:08 PM, Andreas Tosstorff < andreas.tosstorff.cup.uni-muenchen.de> wrote: > Dear all, > > > thank you for your replies! As David pointed out, setting up the > simulation was not the problem, but it's the separation of the two > solvents, as seen in the attached pictures. > > After the suggested google search I came across a paper titled "New > Six-site Acetonitrile Model for Simulations of Liquid Acetonitrile and its > Aqueous Mixtures" by NIKITIN and LYUBARTSEV from 2007 (attached to this > mail). > > They report that they were able to succesfully simulate water-acetonitrile > mixtures with their acetonitrile model. They furthermore state that their > model can easily be included into AMBER. > > So how do I do this? > > Do I write an .frcmod and .lib file for acetonitrile using the parameters > (Lennard-Jones parameters, charge, what else?) they published and then > rebuild my system in tleap? > > > This is completely new to me so I would really appreciate your help! > > > Best, > > Andy > > > > On 04/05/2017 05:00 PM, David Cerutti wrote: > >> 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 >>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >>> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > -- > M.Sc. Andreas Tosstorff > Lehrstuhl für Pharmazeutische Technologie und Biopharmazie > Department Pharmazie > LMU München > Butenandtstr. 5-13 ( Haus B) > 81377 München > Germany > Tel.: +49 89 2180 77059 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > >