[gmx-users] Physical problems of comm removal

[Berk Hess]

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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