Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an optimally packed system and simulate it with the Gromacs 3.3.1 version you can download from http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.3.1-rtc.tgz That version of gromacs has the roto-translational constraints implemented that were developed by Andrea Amadei. Mind that the server is fresh :) The paper is about to be submitted. Unfortunately I haven't had time to dig into the GMX 4 code to implement the rotational constraints yet. I wouldn't want to compromise the performance :S
Cheers, Tsjerk On Fri, Mar 13, 2009 at 8:26 PM, TJ Piggot <t.pig...@bristol.ac.uk> wrote: > You might want to try a rombic dodecahedron box (an option in editconf). > > Or you can run the simulation using a triclinic box hoping the images don't > interact and then check after the simulation has finished using g_mindist > -pi on the trajectory, bearing in mind if they do then you will have wasted > a lot of time. > > If you do want to use a triclinic box having a larger amount of water > surrounding the complex may be advisable as this makes images interacting > less likely > > Tom > > --On Friday, March 13, 2009 20:10:05 +0100 Tsjerk Wassenaar > <tsje...@gmail.com> wrote: > >> Hi, >> >> You have to make sure that you're molecule doesn't rotate. Otherwise >> it will cause direct interactions over the PBC. The same holds true >> for large conformational changes. >> >> Cheers, >> >> Tsjerk >> >> On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> Lucio Montero wrote: >>>> >>>> I want to simulate a protein complex using a triclinic box, because it >>>> reduce my system size in 60%, and consequently the computing time. I >>>> have read that using a triclinic box can give problems for a long MD if >>>> the peptide has a whirl, but I don´t know if it is a problem for a >>>> complex of ~ 530 aa (protein 1: 376 aa, protein 2: 132 aa, protein 3: >>>> 20 aa, complex size 64x64x104 Angstroms) surrounded by 12 Ângstroms of >>>> water. I want to run the MD simulating 20 ns. >>> >>> What problems have you read about? Can you cite a source so we know what >>> you're talking about? >>> >>> -Justin >>> >>>> Best regards, >>>> Lucio Montero >>>> >>>> ---------------------------------------------------------------------- >>>> ---------------------------------------------------------- Lucio >>>> Ricardo Montero Valenzuela >>>> Laboratorio del Dr. Federico Sánchez >>>> Ext. 27666 >>>> Departamento de Biología Molecular de Plantas >>>> Instituto de Biotecnología, UNAM >>>> Cuernavaca, Morelos, 62210 >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-us...@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-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> ICTAS Doctoral Scholar >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@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-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> Junior UD (post-doc) >> Biomolecular NMR, Bijvoet Center >> Utrecht University >> Padualaan 8 >> 3584 CH Utrecht >> The Netherlands >> P: +31-30-2539931 >> F: +31-30-2537623 >> _______________________________________________ >> gmx-users mailing list gmx-us...@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ---------------------- > TJ Piggot > t.pig...@bristol.ac.uk > University of Bristol, UK. > > _______________________________________________ > gmx-users mailing list gmx-us...@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php