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. 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: [email protected] > > To: [email protected] > > 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: [email protected] > > > > To: [email protected] > > > > 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: [email protected] > > > > Web: http://www.bph.rub.de > > > > > > > > _______________________________________________ > > > > gmx-users mailing list [email protected] > > > > 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 [email protected]. > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > ______________________________________________________________________ > > > Express yourself instantly with MSN Messenger! MSN Messenger > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > 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 [email protected]. > > > 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: [email protected] > > Web: http://www.bph.rub.de > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ______________________________________________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > 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: [email protected] Web: http://www.bph.rub.de _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
