From: Evandro Semighini (epsemighini_at_gmail.com)
Date: Sun Jul 19 2015 - 21:42:17 CDT
Thank you !
I misstyped at the other mail, I meant to say PBC and not PME, sorry.
Thank you for the explanation and the patience.
2015-07-19 23:13 GMT-03:00 Peter Freddolino <petefred_at_umich.edu>:
> Dear Evandro,
> Let’s be clear, this behavior should not be different with the charmm or
> amber force field. If you have properly configured periodic boundary
> conditions, this is just an effect of how you’ve set up coordinate wrapping.
> Also, PME (particle mesh Ewald) requires PBCs (periodic boundary
> conditions), but the inverse is not true. PME just has to do with long
> range electrostatics calculations, and will not alter wrapping. Please do
> not confuse these two things.
> You need to carefully inspect your system to make sure that when properly
> viewing it in the presence of the periodic boundaries you have configured,
> it is correct; I can’t make any guarantees just on the basis of hearing
> about a case, but I can tell you that the symptoms you’ve described are
> usually just because people don’t realize the effects of various choices of
> wrapping parameters.
> > On Jul 17, 2015, at 8:44 AM, Evandro Semighini <epsemighini_at_gmail.com>
> > Hello Peter,
> > Thank you !
> > I really thought this strange, because using CHARMM FF this two things
> never happened to me or my co-workers, and because PME was always set in my
> simulations, so, I was expecting that the part of the protein that gone out
> of the box would be "teleported" to the other side of the system. I always
> imagined how it will mess up RMSD measurements.
> > Yes, I saw the deformations on the water box you said, and I imagined it
> happened due to the empty space left by the protein at that volume.
> > So, it's more a issue with visualization of the system, since I am using
> PME, and the protein goes trough the MD normally?
> > Thank you for the tip of pbctools and periodic images, I saw it
> yesterday was waiting the "out of box" run finish to have more material to
> work with.
> > Thank you again !
> > Evandro
> > 2015-07-16 23:54 GMT-03:00 Peter Freddolino <petefred_at_umich.edu>:
> > Hi Evandro,
> > The key here is that you’re simulating a periodic system. You don’t have
> just one box, but an infinite number of identical boxes tiled through
> space. So when your waters appear to go out of the box when wrap is off,
> they’ve just gone into the next periodic copy over (but it is replaced by a
> copy coming in through the other side, so the contents of your unit cell
> are constant). When you have wrap on, your protein may appear to stick out
> of the box because it hasn’t moved far enough to be wrapped. You should see
> a complementary gap in the water on the opposite side of the system where
> it is occupying space. Viewing your system with the help of the pbctools
> plugin, or with periodic images turned on (in the ‘periodic’ tab of the
> graphical representations menu), can help to see what the system really
> looks like.
> > Best,
> > Peter
> > > On Jul 16, 2015, at 3:21 PM, Evandro Semighini <epsemighini_at_gmail.com>
> > >
> > > Hello,
> > >
> > > I am running NAMD using AMBER Force Field and I am facing a issue with
> the water box.
> > >
> > > I measured the water vectors and size with VMD and configured the
> periodic boundary conditions as described at the tutorials, and ran a
> simulation, without defining PMEGridSize and using wrap comands.
> > > The simulation goes well, except that the water molecules diffuses a
> lot away from the box, they seems to evaporate.
> > >
> > > I used then the wrapWater and wrapAll comands and things got more
> strange, as the protein is entirely removed from the water box after energy
> minimization, but the MD runs ok after that.
> > >
> > > I checked the data from the cell vectors and center, as well as the
> coordinate files and the numbers are within the expected values.
> > >
> > > The minimization seems to reset the coordinates of the protein.
> > >
> > > Can anyone, please, point me where I am missing ?
> > >
> > > Thank you,
> > > Evandro
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