Dave - wow thank you very much!
I did not know you can do vacuum simulations with PBC - that is great news
(if I am reading that correctly)
I get your point about the previous paper being a duct tape approach -
interesting approach though
I will soon try your suggestions and get back to you!
Much appreciation - hope you are doing well in Michigan!
~Kenneth
Kenneth N. McGuinness Ph.D
Research Associate
Advanced Science Research Center CUNY
Adviser: Dr. Rein Ulijn <http://www.ulijnlab.com/>
Cell: 928-925-7693
On Mon, Apr 4, 2016 at 3:33 PM, David Cerutti <dscerutti.gmail.com> wrote:
> OK, so reading the Gromacs manual (which is a really good how-to on many
> things MD, I might add), I see Sphere (g = 1) and Cylinder (g = 2), so from
> the rest of your message I am assuming you meant "option (g=1 sphere)."
> That's something that Amber can do, but if your system is up to 10,000
> atoms then depending on the type of cutoffs you want (a raw Coulomb
> interaction will run into lots of problems) you may be better off going to
> periodic boundary conditions already. Vacuum simulations are NOT
> absolutely faster than simulations in water. The problem is that vacuum
> simulations often require a big cutoff to the tune of 15 or 18 Angstroms,
> compared to condensed-phase simulations with PBC which take short cutoffs
> and the O(N log N) P3M interactions (also called PME).
>
> Another thing to note is that, if all you want is for the molecules to be
> confined to a particular region, periodic boundary conditions with NVT
> (fixed number of particles, volume, and temperature) or NVE (canonical
> ensemble, fixed particle count, volume, and energy) will also give you this
> effect. If a particle tries to wander out one side of the box, it just
> checks back in the other and sees the same neighbors it used to, perhaps
> from a different side. Welcome to the Hotel Periodic.
>
> So if you just want to see molecules bumping into each other in a confined
> space I would recommend just taking NVT in PBC, with PMEMD. No spherical
> restraint force necessary--the paper you cite sounds like it's using a
> duct-tape way to emulate stochastic boundary conditions, but the artifacts
> you get are not necessarily any more benign than what would happen with
> PBCs. If you just want to put in a number of copies of each molecule and
> watch the structures they form, make your boxes cubic, create some PDB
> structures of your INDIVIDUAL molecules, and use my AddToBox utility to
> randomly place multiple copies of them around a box of your liking. This
> will give you a PDB file with an initial structure. For vacuum
> simulations, use the tleap command "setBox x vdw 10.0" (where x is the name
> of the structure you read in, as in "x = loadPdb <name of PDB>"). For
> solution phase simulations, use AddToBox again to add water in the
> proportion you want (tleap's solvateBox will not necessarily place the
> amount of water you're looking for if there is a target molality). In all
> cases, use ChBox to edit the final box dimensions of your system back to
> whatever you were using in with AddToBox (tleap will make its own judgments
> about what the box dimensions should be, but AddToBox knows about PBCs
> already so you can reset the box dimensions).
>
> When you simulate, for the vacuum case and optimal speed I'd recommend
> bumping up the cutoff and decreasing the grid density proportionately. If
> you're happy enough with the accuracy of the default settings, bump the
> cutoff up to 12 and select a value of nfft1, nfft2, and nfft3 (remember,
> cubic box) that gives you a grid spacing just shy of 1.5A. That will cut
> down on the reciprocal space work by up to three times depending on how
> much empty space is in your simulations. For condensed phase simulations,
> just stick to the default run conditions (these will be 8A cutoff, grid
> spacing just shy of 1A).
>
> Dave
>
>
> On Mon, Apr 4, 2016 at 2:52 PM, Kenneth McGuinness <
> kenneth.mcguinness.gmail.com> wrote:
>
> > Hey Dave - great to hear from you!
> >
> > I wrote my comments in-line to help with following the conversation
> >
> >
> >
> > On Mon, Apr 4, 2016 at 2:32 PM, David Cerutti <dscerutti.gmail.com>
> wrote:
> >
> > > Hi Ken!
> > >
> > > The best advice I can give here is that Amber isn't a program that does
> > > hard-sphere potentials, so if you want particles to suddenly hit an
> > > infinite wall when they travel within (or outside of) some distance of
> > one
> > > another you'll need a separate code.
> >
> >
> > The type of potential I am looking to implement is the one implemented in
> > section 4.3.2 with option (g=2 sphere) in this link:
> >
> > ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf
> >
> > I tried gromacs but it does not implement GPU usage yet with vacuum/and
> no
> > pbc -speed is the biggest need right now- Amber does conveniently
> >
> >
> >
> > > The closest you could get would be to
> > > use the nmropt (NMR optimization) features to implement HARMONIC
> > restraints
> > > on either side of a flat-bottom potential.
> >
> >
> > Not sure how to do this in a 3D sense (spherical) in terms of the DISANG
> > options and restraint files (gromacs has a simple format) I have not
> > wrapped my head around Amber's way of doing it yet :-)
> >
> > Particles connected by such a
> > > potential experience no forces (at least, no forces due to one another)
> > so
> > > long as they are within some small distance of on another, but begin to
> > > experience harmonic attraction as the distance crosses that threshold.
> > >
> > > Depending on what exactly you want to simulate, I can recommend
> different
> > > programs. How many particles (atoms) will your system have?
> >
> >
> > ~1000-10,000 atoms
> >
> >
> > > Do you want
> > > periodic boundary conditions, to simulate the effect of having a fairly
> > > elaborate density of material, or are you content to see just a few of
> > > these molecules interact in the gas phase, off in an otherwise empty
> > region
> > > of space?
> > >
> >
> > I am setting up a screening process for molecular interactions
> >
> > 1. Speed is the most important part so I intend on using the gas phase
> > without periodic boundaries
> > 2. Once I see interactions worth pursuing in (1) I will then add more
> > molecular details (implicit, explicit solvent, pbc etc.) in the force
> field
> > to rule out interactions worth testing in the lab.
> > 3. The spherical potentials prevent the molecules from drifting too far
> > into space because of the lack of viscosity
> >
> > I am really grateful for your time!
> >
> > Any more details I can give? Please lmk
> >
> > Thank you Dave!
> >
> >
> >
> >
> > >
> > > Dave
> > >
> > >
> > > On Mon, Apr 4, 2016 at 2:03 PM, Kenneth McGuinness <
> > > kenneth.mcguinness.gmail.com> wrote:
> > >
> > > > Hi everyone,
> > > >
> > > > This is my first post to this forum and I am grateful to be a part of
> > it!
> > > >
> > > > I am relatively new to Amber as well. Sorry if this post goes over
> > > material
> > > > that someone else has posted before. I have looked as far as I could
> > and
> > > I
> > > > did not find an exact match on what I am looking to do.
> > > >
> > > > So without going into the entire project,
> > > >
> > > > I would like to run simulations in vacuo using spherical flatwell
> > > > potentials.
> > > >
> > > > I am not sure how to implement this - however this article has
> > > implemented
> > > > the method (this paper is similar to my work - and the method will
> > > greatly
> > > > help my work)
> > > >
> > > > http://pubs.acs.org/doi/abs/10.1021/jp501503x
> > > >
> > > > Any help in setting this up would be very much appreciated - I am
> still
> > > > trying to decipher what section 24.1 means in the Amber doc. Please
> let
> > > me
> > > > know any details that are needed from me in order to progress.
> > > >
> > > > I greatly appreciate any and all help!
> > > >
> > > > Thank you!
> > > >
> > > > With gratitude,
> > > >
> > > > ~Kenneth
> > > >
> > > > Kenneth N. McGuinness Ph.D
> > > > Research Associate
> > > > Advanced Science Research Center CUNY
> > > > Adviser: Dr. Rein Ulijn <http://www.ulijnlab.com/>
> > > > Cell: 928-925-7693
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Received on Mon Apr 04 2016 - 15:00:03 PDT
