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Hi,<br><br>The cleanest solution is using a rhombic dodecahedron:<br>volume 13.58^3/sqrt(2) = 1771 nm^3<br>(I don't know why people still consider truncated octahedrons).<br><br>You can try using comm-mode=angular with as comm group only the protein.<br>This should not produce significant artifacts when your protein is large.<br>However, this will not run with domain decomposition,<br>only with particle decomposition (mdrun -pd), which scales worse,<br>but probably not so bad with 4-8 cores.<br><br>Berk<br><br>> Date: Thu, 12 Feb 2009 16:00:30 +0100<br>> From: cseifert@bph.ruhr-uni-bochum.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Physical problems of comm removal<br>> <br>> Hi users!<br>> <br>> I simulate a stretched protein in TIP4P water in a cubic box<br>> (6.83x9.60x13.58=890) with pbc. During a 50 ns simulation, my protein<br>> must not rotate (otherwise, it will interact with itself). I found three<br>> possibilities to avoid a self interaction: (1) a bigger box, (2)<br>> restraints or (3) comm removal.<br>> <br>> In details:<br>> (1) bigger box:<br>> I need at least a diameter of 13.58 nm in every direction to avoid a<br>> self interaction (because of a possible rotation of the protein). For a<br>> cubic box, this would be (13.58^3 =) 2504 nm^3. For a truncated<br>> octahedron still 1928 nm^3, which would still be twice the box size I<br>> use now. This is not suitable for me.<br>> <br>> (2) restraints:<br>> These are "long-time" runs, where I want to observe domain movement, so<br>> restraints are not an alternative for my simulation.<br>> <br>> (3) comm removal:<br>> To use my stretched box, I have to use COMM-MODE = Angular. This mode<br>> provokes artifacts, if I use it only on my protein and is therefore<br>> forbidden since GMX4.0.3. But what happens, if I use it for my whole<br>> system? My protein has a mass of 142800 a.m.u. and the solvent has a<br>> mass of 998100 a.m.u. Let us assume, that the solvent movement reduces<br>> itself, because its movement is undirected and the mass of the protein<br>> is high enough to fall into account (which might not be true because:<br>> <br>> v_{comm_removal}= 1 / (m_{solvent} + m_{protein}) \cdot<br>> \sum_{i(solvent)}^n{(solvent)} ( m_i \cdot v_i) \cdot<br>> \sum_{j(protein)}^o{(protein)} ( m_j \cdot v_j)<br>> <br>> with \sum v_i=0 (because the movement of the solvent is undirected) the<br>> equation would be:<br>> <br>> v_{comm_removal}= 1 / (m_{solvent} + m_{protein}) \cdot <br>> \sum_{j(protein)}^o{(protein)} ( m_j \cdot v_j)<br>> <br>> which weights the movement of the protein with its mass, put divides it<br>> by the mass of protein+mass, what may result in a to small removal of<br>> the comm.)<br>> <br>> Beside this problem, do I have to expect that there might be other<br>> problems with COMM-MODE = Angular, COMM-GRPS = System and a cubic box<br>> with pbc?<br>> <br>> <br>> <br>> -- <br>> M. Sc. Christian Seifert<br>> Department of Biophysics<br>> University of Bochum<br>> ND 04/67<br>> 44780 Bochum<br>> Germany<br>> Tel: +49 (0)234 32 28363<br>> Fax: +49 (0)234 32 14626<br>> E-Mail: cseifert@bph.rub.de<br>> Web: http://www.bph.rub.de<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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