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 >
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