# [gmx-users] Physical problems of comm removal

XAvier Periole x.periole at rug.nl
Thu Feb 12 20:18:31 CET 2009

On Feb 12, 2009, at 8:03 PM, Justin A. Lemkul wrote:

>
>
> 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.
>> >
>> > 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.
I agree with this, the z axis has been use full. If allowing to choose
is not
too much work this would be really good.

XAvier.

>
> -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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>> > > > >
>> > > > >
>> > >
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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
> 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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