[gmx-users] Physical problems of comm removal

[Christian Seifert]

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
> > 
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> ______________________________________________________________________
> Express yourself instantly with MSN Messenger! MSN Messenger
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
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