Hi, what do you mean: "use gmxdump to trace the molecule"? I'm a beginner with gromacs and all I found about gmxdump is that it reads a binary file & prints that to standard output in a readable format. So how can I check if my atom number is the same in my pdb file & my output file?
Carla On Wed, Sep 30, 2009 at 4:38 AM, Itamar Kass <itamar.k...@gmail.com> wrote: > Hi, > > another point you should consider is that the atom/molecule number in the > pdb or gro file are not necessarally the what you see in your output. You > should use gmxdump in such cases to trace the molecule. > > > Cheers, > Itamar > > --- > > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > =========================================== > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@med.monash.edu.au > ============================================ > > > On Wed, Sep 30, 2009 at 1:14 AM, Manik Mayur <manik.ma...@gmail.com>wrote: > >> 2009/9/29 Justin A. Lemkul <jalem...@vt.edu> >> >>> >>> >>> Carla Jamous wrote: >>> >>>> >>>> Thank you for your reply, >>>> but none of the water molecules with error messages is trapped inside my >>>> protein, nor is it in contact with the protein or the ions in my system. >>>> >>>> >> Also if the water molecules are positioned properly, you can try define = >> -DPOSRES_WATER in your .mdp file with a high value set in your >> topology(.top) file under [position restraint] section as, >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 100000 100000 100000 >> #endif >> >> -Manik >> >> Then you need to watch the trajectory and see where things go wrong. In >>> unstable systems, I often set "nstxout = 1" to capture as many frames in the >>> .trr file as possible (if the crash is happening early, as it is in your >>> case). >>> >>> Likely, energy minimization did not resolve all the bad contacts, but may >>> still have converged within your criteria. You could also specify a lower >>> target Fmax during EM to see if things resolve. >>> >>> -Justin >>> >>> Carla >>>> >>>> On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar >>>> <tsje...@gmail.com<mailto: >>>> tsje...@gmail.com>> wrote: >>>> >>>> Hi Carla, >>>> >>>> You may have a water molecule trapped inside your protein. Check the >>>> water molecule with the given atom number in a viewer, together with >>>> your structure. If it is inside, you can try to remove it manually >>>> from the system, editing the structure file and decreasing the amount >>>> of solvent listed in te topology file. If you edit the .gro file, do >>>> mind to decrease the number on the second line (the number of atoms) >>>> by three. >>>> >>>> Hope it helps, >>>> >>>> Tsjerk >>>> >>>> On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous >>>> <carlajam...@gmail.com <mailto:carlajam...@gmail.com>> wrote: >>>> > Hi, >>>> > I have a problem with water molecules in my system: I'm using >>>> Gromacs with >>>> > ffamber94 force-field. During minimization, I have this message: >>>> > >>>> > t = 0.014 ps: Water molecule starting at atom 10045 can not be >>>> settled. >>>> > Check for bad contacts and/or reduce the timestep.Wrote pdb files >>>> with >>>> > previous and current coordinates >>>> > >>>> > The minimization converged. However, molecular dynamics were >>>> stopped. >>>> > I tried minimization with different parameters: Flexible, >>>> > position-restrained, reducing my timestep, etc... and nothing >>>> worked. >>>> > >>>> > I also tried one simulation with TIP3P water model and another >>>> simulation >>>> > with SPC water model and I still get the same error. >>>> > I tried to access: oldwiki.gromacs.org >>>> <http://oldwiki.gromacs.org> but access is denied. >>>> > >>>> > Please does anyone have a solution to propose? >>>> > >>>> > Thanks >>>> > Carla >>>> > >>>> > _______________________________________________ >>>> > gmx-users mailing list gmx-users@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> > http://lists.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 >>>> <mailto: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 >>>> <mailto:gmx-users@gromacs.org> >>>> http://lists.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 >>>> <mailto:gmx-users-requ...@gromacs.org>. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.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 >>> Ph.D. Candidate >>> 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-users@gromacs.org >>> http://lists.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 >>> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.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 >> > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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