You're welcome. Forgot to mention that it comes with an additional .mdp option (rototr = yes/no). That does break compatibility with other versions regarding reading .tpr files.
Cheers, Tsjerk On Fri, Mar 13, 2009 at 10:48 PM, TJ Piggot <[email protected]> wrote: > This looks great thanks, had meant to try and implement something like these > restraints for ages but never got round to it, you know how it is ... > > Tom > > --On 13 March 2009 21:06 +0100 Tsjerk Wassenaar <[email protected]> wrote: > >> 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 <[email protected]> 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 >>> <[email protected]> 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 <[email protected]> >>>> 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 [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 >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> 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 [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 >>>>> >>>> >>>> >>>> >>>> -- >>>> 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 [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 >>> >>> >>> >>> ---------------------- >>> TJ Piggot >>> [email protected] >>> University of Bristol, UK. >>> >>> _______________________________________________ >>> 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 >>> >> >> >> >> -- >> 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 [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 > > > > ---------------------- > TJ Piggot > [email protected] > University of Bristol, UK. > > _______________________________________________ > 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 > -- 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 [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. 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