From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 03 2012 - 06:02:39 CST
Without pbc water diffuses, but that's not important for namd to continue, as long as you continue without pbc too, otherwise the atoms get wrapped to position where they are not expected, So it's not a fail by NAMD. With other words: When using PBC the atoms that leave the box, are threated as they come from the other side into the box again. If not using pbc, they just go away. When then restart with such a restart and PBC used, theres to place for the diffused atoms in the cell to get wrapped to, so you will get large forces in VDW. For such a system you should always use pbc I would say, even because pressure is relevant, isn't it??
Then for pressure controlled runs, you should use constantarea (only change Z dimension).
Mit freundlichen Grüßen
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von R. Charbel Maroun
> Gesendet: Freitag, 3. Februar 2012 11:58
> An: Norman Geist
> Cc: 'Boyang Wang'; Namd Mailing List
> Betreff: Re: AW: namd-l: Energy minimization of membrane
>
> Hi,
>
> Thanks for the feedback. It's not that I didn't want to use PBC. I
> just wanted to know if it was necessary for a minimization. By the
> way, before running MD, the system must be well minimized, otherwise
> it might become unstable during the trajectory. It's part of the
> equilibration step, before production.
>
> I used CHARMM-GUI for building my membrane system. I ran last night an
> energy minimization with PME and PBC for just the
> water molecules and the K and Cl ions; lipids and receptor fixed (when
> you use PME you need PBC). The question is what values to use for
> PMEGridSize and cellBasisVector? What I did is that for the first set
> I measured approximately on the screen the dimensions of the box size;
> for the second set I just guessed slightly larger values. I don't know
> if that's right.
>
> The results of the minimization show that the ordered structure of
> waters away from the phospholipid head groups was lost (good!). The
> water layers above and below got flattened, more compact along the
> axis perpendicular to the membrane, and wider in the axes of the
> membrane. When I ran a minimization without PBC, one water molecule
> would always escape from the box and get wild coordinates. NAMD would
> then stop if you tried to use this coordinate set for further
> calculations.
>
> # PBC
> cellBasisVector1 90.0 0.0 0.0
> cellBasisVector2 0.0 109.0 0.0
> cellBasisVector3 0.0 0.0 90.0
> cellOrigin 0.0 0.0 2.0
> wrapAll on
> wrapWater on
> dcdUnitCell yes
>
> # PME
> PME yes
> PMEGridSizeX 85
> PMEGridSizeY 85
> PMEGridSizeZ 103
>
>
> Any suggestions ?
>
> Cheers,
>
> C Maroun
>
> Norman Geist <norman.geist_at_uni-greifswald.de> a écrit :
>
> > Hi,
> >
> >
> >
> > I'm not a specialist in bio chemistry, more on IT, but I would expect
> your
> > membrane as not big enough to be realistic without its periodic
> copys. So it
> > won't behave good, as it would be in vacuum, and the best energy
> > conformation achieved then, wouldn't be the one you want. I would
> expect
> > that it will relax more into a strange conformation, as in a
> realistic one.
> > Also, if you don't set PBC, your solvent will diffuse away, if there
> is one.
> >
> >
> >
> > What's the reason for not want to set PBC in minimization? If you
> want to
> > look if your system want to expand, you can try that out with some
> different
> > box sizes, and with dynamics, not minimization as minimization will
> not move
> > the system much.
> >
> >
> >
> > Correct me if required ;)
> >
> >
> >
> > Best wishes
> >
> >
> >
> > Norman Geist.
> >
> >
> >
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag
> > von Boyang Wang
> > Gesendet: Freitag, 3. Februar 2012 06:31
> > An: R. Charbel Maroun
> > Cc: namd-l_at_ks.uiuc.edu
> > Betreff: Re: namd-l: Energy minimization of membrane
> >
> >
> >
> > Hi Charbel,
> >
> >
> >
> > I think PBC is necessary, but keep in mind that calculations will be
> much
> > slower.
> >
> >
> >
> > Best,
> >
> > Boyang
> >
> >
> >
> > On Thu, Feb 2, 2012 at 8:37 PM, R. Charbel Maroun
> <charbel.maroun_at_inserm.fr>
> > wrote:
> >
> > Hello,
> >
> > When we do energy minimization with NAMD of a protein-membrane
> system,
> > do we have to give PBC in the script, just like for a
> > molecular dynamics calculation or is this implicitely taken into
> > consideration? If not, that means that the protein-membrane system is
> > in vacuum and could become unstable during minimization.
> >
> > Greetings,
> >
> > C Maroun
> >
> >
> >
> >
> > ----------------------------------------------------------------
> > This message was sent using IMP, the Internet Messaging Program.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > Boyang Wang, Ph.D.
> >
> >
>
>
>
>
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
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