This is the mdp file i use for my energy minimization Thanks Carla ; ; 1W5B all-atom ; Input file ; cpp = /usr/bin/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 500 ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01
nstcomm = 1 ns_type = grid nstlist = 10 nstxout = 1 rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = no Pcoupl = no gen_vel = no On Fri, Oct 2, 2009 at 12:46 PM, Jochen Hub <[email protected]> wrote: > Carla Jamous wrote: > >> Hi, >> when I get the error message: "water molecule cannot be settled",does it >> have to do with the SETTLE parameter in gromacs? >> If yes, does anyone know how to fix this? >> > No, that probably means that you have clashes (atomic overlaps) in your > system which cause huge forces. Track down which atoms cause the error > message and remove the clashes. > > If that error message appeares during energy minimization, using flexible > water may help. Define -DFLEXIBLE in the mdp file, and check in the > spc/itp4p/tip3p.itp file if flexible water molecules are actually defined. > > Good luck, > Jochen > > > > >> Carla >> >> On Thu, Oct 1, 2009 at 4:46 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Carla Jamous wrote: >> >> Hi, >> I have a problem, I'm running EM, it works but when it comes >> to doing position-restrained MD, it gives me this error message: >> >> Segmentation fault >> Large VCM(group System): -1293135642624.00000, >> 358859374592.00000, -846768177152.00000, T-cm: 6.13428e+26 >> >> I searched the archives, it says to check-out: >> oldwiki.gromacs.org <http://oldwiki.gromacs.org> >> <http://oldwiki.gromacs.org> >> >> but this site doesn't exist anymore. >> >> >> All of the content has been moved to the new site, albeit a very >> different organization system. You should still be able to find >> it with a bit of digging. >> >> >> So please can anyone give me the answer to this problem? >> >> >> The problem is that your system is suddenly moving very fast, >> probably blowing up. Without a further description of the system >> and seeing your .mdp file, it's hard to say what the root problem is. >> >> -Justin >> >> >> Cheers, >> 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 >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> 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 >> > > > -- > --------------------------------------------------- > Dr. Jochen Hub > Molecular Biophysics group > Dept. of Cell & Molecular Biology > Uppsala University. Box 596, 75124 Uppsala, Sweden. > Phone: +46-18-4714451 Fax: +46-18-511755 > > --------------------------------------------------- > > _______________________________________________ > 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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