Hi Prof. David. What details do you mean? Actual topology files are attached. Anything else?
Thanks a lot in advance! Sincerally yours, Jones On 10/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > Jones de Andrade wrote: > > Thanks Prof. David. > > > > I've done all that now, but at the moment I'm locked getting lots of the > > "lovelly" error: > > > > Warning: 1-4 interaction between 7 and 16 at distance 4.302 which is > > larger than the 1-4 table size 1.000 nm > > These are ignored for the rest of the simulation > > This usually means your system is exploding, > > if not, you should increase table-extension in your mdp file > > step 0Segmentation fault > > please give more details... > > > > > > I've visually checked the .gro file, and the atoms mentioned are not > > from start at such crazy distances. I've included extra exclusions > > between the virtual sites and the atoms that are at "one" and "two" > > "bonds" away. > > > > Does it means I should include also the 1-4 in the exclusions or pair > > sections? Sorry, never dealt with dummy sites before this. I thought > > using a pre-equilibrated box with a different model would at least avoid > > explosion problems, so or I missing something, of this assumption was > > completelly wrong. > > > > Thanks a lot in advance, > > > > Sincerally yours > > > > Jones > > > > On 10/11/07, *David van der Spoel* <[EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>> wrote: > > > > Jones de Andrade wrote: > > > Hi all. > > > > > > Well, I'm having a bit of trouble here because the work has > > decided to > > > go in the direction of something I've never used before with > gromacs: > > > dummy atoms (or now "virtual sites"). > > > > I assume this is not for a protein, in which case pdb2gmx does it > > for you. > > > > > > I've got at least three questions in order to use them: > > > > > > 1 - does the virtual sites need to be included in the .gro files > in > > > order to make a simulation run? > > > > > Yes. > > > > > 2 - do I need to include them in the "exclusion list"? > > It depends, but usually yes. > > > > > > > > 3 - do I need to include them in the "atoms" section? > > Yes. > > > > > > > > > > > Thanks a lot in advance for any help anyone can provide in these > > > subjects. ;) > > Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P > etc. > > > > > > > > > > Sincerally yours, > > > > > > Jones > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > <mailto: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 [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > <http://www.gromacs.org/mailing_lists/users.php> > > > > > > -- > > David. > > > ________________________________________________________________________ > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > > Dept. of Cell and Molecular Biology, Uppsala University. > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > phone: 46 18 471 4205 fax: 46 18 511 755 > > [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > <mailto: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 [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
simu.298K.017.mdp
Description: Binary data
C06H12.itp
Description: Binary data
C06H12.top
Description: Binary data
ff_amber_perHC.itp
Description: Binary data
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