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: [email protected] ============================================ On Wed, Sep 30, 2009 at 1:14 AM, Manik Mayur <[email protected]> wrote: > 2009/9/29 Justin A. Lemkul <[email protected]> > >> >> >> 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 <[email protected]<mailto: >>> [email protected]>> 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 >>> <[email protected] <mailto:[email protected]>> 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 [email protected] >>> <mailto:[email protected]> >>> > 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 [email protected] >>> <mailto:[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] >>> <mailto:[email protected]> >>> 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 [email protected] >>> <mailto:[email protected]>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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