[gmx-users] Physical problems of comm removal
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 12 20:03:53 CET 2009
Berk Hess wrote:
>
>
> > Date: Thu, 12 Feb 2009 16:49:33 +0100
> > From: cseifert at bph.ruhr-uni-bochum.de
> > To: gmx-users at gromacs.org
> > Subject: RE: [gmx-users] Physical problems of comm removal
> >
> > Thanks for your ideas!
> >
> > I will discuss the possible solutions with my supervisor.
> >
> > To your PS:
> > This is a good hint, I changed many optimization flags to get a good
> > scaling but never changed the axis. I created the box with editconf
> > -princ. It automatically made z the longest axis and x the shortest.
> > Since many users use PME, it might be a good idea to change the behavior
> > of editconf -princ.
> >
>
> Ah, I didn't know this.
> I changed the order of -princ for 4.0.4.
>
Could the -princ option be made interactive, such that the user could choose the
axis? I use -princ to orient the long axis of my membrane proteins along the
z-axis, since the bilayer is in the x-y plane. I suppose a bit of rotation
could fix this, but allowing the user to choose would be pretty convenient.
-Justin
> Berk
>
> > Again: Thank you very much for your help!
> > Christian.
> >
> > On Thu, 2009-02-12 at 16:28 +0100, Berk Hess wrote:
> > > Hi,
> > >
> > > Another crude solution is to divide your protein into two groups along
> > > the long axis
> > > and use the pull code to keep the two components perpendicular to the
> > > axis
> > > of the vector between the COMs at zero.
> > >
> > > PS: if you have PME your system will run faster when you make x the
> > > long axis.
> > >
> > > Berk
> > >
> > > > Date: Thu, 12 Feb 2009 16:21:29 +0100
> > > > From: cseifert at bph.ruhr-uni-bochum.de
> > > > To: gmx-users at gromacs.org
> > > > Subject: RE: [gmx-users] Physical problems of comm removal
> > > >
> > > > Hi Berk,
> > > >
> > > > the rhombic dodecahedron with 1771 nm^3 is still twice as big as my
> > > > stretched box.
> > > >
> > > > This System scales quite well till 256 CPUs and I normally use this
> > > > amount of CPUs (I have to hurry up with my PhD thesis), so particle
> > > > decomposition is not an alternative.
> > > >
> > > > Are there other alternatives?
> > > >
> > > > Thanks so far!
> > > > Christian
> > > >
> > > > On Thu, 2009-02-12 at 16:09 +0100, Berk Hess wrote:
> > > > > Hi,
> > > > >
> > > > > The cleanest solution is using a rhombic dodecahedron:
> > > > > volume 13.58^3/sqrt(2) = 1771 nm^3
> > > > > (I don't know why people still consider truncated octahedrons).
> > > > >
> > > > > You can try using comm-mode=angular with as comm group only the
> > > > > protein.
> > > > > This should not produce significant artifacts when your protein is
> > > > > large.
> > > > > However, this will not run with domain decomposition,
> > > > > only with particle decomposition (mdrun -pd), which scales worse,
> > > > > but probably not so bad with 4-8 cores.
> > > > >
> > > > > Berk
> > > > >
> > > > > > Date: Thu, 12 Feb 2009 16:00:30 +0100
> > > > > > From: cseifert at bph.ruhr-uni-bochum.de
> > > > > > To: gmx-users at gromacs.org
> > > > > > Subject: [gmx-users] Physical problems of comm removal
> > > > > >
> > > > > > Hi users!
> > > > > >
> > > > > > I simulate a stretched protein in TIP4P water in a cubic box
> > > > > > (6.83x9.60x13.58=890) with pbc. During a 50 ns simulation, my
> > > > > protein
> > > > > > must not rotate (otherwise, it will interact with itself). I
> > > found
> > > > > three
> > > > > > possibilities to avoid a self interaction: (1) a bigger box, (2)
> > > > > > restraints or (3) comm removal.
> > > > > >
> > > > > > In details:
> > > > > > (1) bigger box:
> > > > > > I need at least a diameter of 13.58 nm in every direction to
> > > avoid a
> > > > > > self interaction (because of a possible rotation of the
> > > protein).
> > > > > For a
> > > > > > cubic box, this would be (13.58^3 =) 2504 nm^3. For a truncated
> > > > > > octahedron still 1928 nm^3, which would still be twice the box
> > > size
> > > > > I
> > > > > > use now. This is not suitable for me.
> > > > > >
> > > > > > (2) restraints:
> > > > > > These are "long-time" runs, where I want to observe domain
> > > movement,
> > > > > so
> > > > > > restraints are not an alternative for my simulation.
> > > > > >
> > > > > > (3) comm removal:
> > > > > > To use my stretched box, I have to use COMM-MODE = Angular. This
> > > > > mode
> > > > > > provokes artifacts, if I use it only on my protein and is
> > > therefore
> > > > > > forbidden since GMX4.0.3. But what happens, if I use it for my
> > > whole
> > > > > > system? My protein has a mass of 142800 a.m.u. and the solvent
> > > has a
> > > > > > mass of 998100 a.m.u. Let us assume, that the solvent movement
> > > > > reduces
> > > > > > itself, because its movement is undirected and the mass of the
> > > > > protein
> > > > > > is high enough to fall into account (which might not be true
> > > > > because:
> > > > > >
> > > > > > v_{comm_removal}= 1 / (m_{solvent} + m_{protein}) \cdot
> > > > > > \sum_{i(solvent)}^n{(solvent)} ( m_i \cdot v_i) \cdot
> > > > > > \sum_{j(protein)}^o{(protein)} ( m_j \cdot v_j)
> > > > > >
> > > > > > with \sum v_i=0 (because the movement of the solvent is
> > > undirected)
> > > > > the
> > > > > > equation would be:
> > > > > >
> > > > > > v_{comm_removal}= 1 / (m_{solvent} + m_{protein}) \cdot
> > > > > > \sum_{j(protein)}^o{(protein)} ( m_j \cdot v_j)
> > > > > >
> > > > > > which weights the movement of the protein with its mass, put
> > > divides
> > > > > it
> > > > > > by the mass of protein+mass, what may result in a to small
> > > removal
> > > > > of
> > > > > > the comm.)
> > > > > >
> > > > > > Beside this problem, do I have to expect that there might be
> > > other
> > > > > > problems with COMM-MODE = Angular, COMM-GRPS = System and a
> > > cubic
> > > > > box
> > > > > > with pbc?
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > M. Sc. Christian Seifert
> > > > > > Department of Biophysics
> > > > > > University of Bochum
> > > > > > ND 04/67
> > > > > > 44780 Bochum
> > > > > > Germany
> > > > > > Tel: +49 (0)234 32 28363
> > > > > > Fax: +49 (0)234 32 14626
> > > > > > E-Mail: cseifert at bph.rub.de
> > > > > > Web: http://www.bph.rub.de
> > > > > >
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> > > > --
> > > > M. Sc. Christian Seifert
> > > > Department of Biophysics
> > > > University of Bochum
> > > > ND 04/67
> > > > 44780 Bochum
> > > > Germany
> > > > Tel: +49 (0)234 32 28363
> > > > Fax: +49 (0)234 32 14626
> > > > E-Mail: cseifert at bph.rub.de
> > > > Web: http://www.bph.rub.de
> > > >
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> > --
> > M. Sc. Christian Seifert
> > Department of Biophysics
> > University of Bochum
> > ND 04/67
> > 44780 Bochum
> > Germany
> > Tel: +49 (0)234 32 28363
> > Fax: +49 (0)234 32 14626
> > E-Mail: cseifert at bph.rub.de
> > Web: http://www.bph.rub.de
> >
> > _______________________________________________
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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