Yes I read somewhere that treating the simulation space as a cube has some drawbacks. I'll try these parameters.
On Mon, Mar 9, 2009 at 3:36 PM, Andrew Voronkov <drugdes...@yandex.ru> wrote: > I've used this tutorial: > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf > > I've used command line: editconf -c -f conf.gro -bt dodecahedron -d 0.7 -o > box.gro to center the protein, but the problem remains - protein is still in > the edge of the water box. > > There is also 1-4 warning for which I see no reasons and very fast presision > reached time. > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+01 > Number of steps = 200 > Warning: 1-4 interaction between 2 and 21 at distance 6.197 which is larger > than the 1-4 table size 2.000 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 > or with user tables increase the table size > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.82932e+24 Fmax= inf, atom= 4 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 10 > > Double precision normally gives you higher accuracy. > You might need to increase your constraint accuracy, or turn > off constraints alltogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 10. > Potential Energy = 2.8293175e+24 > Maximum force = inf on atom 4 > Norm of force = inf > > gcq#239: "killing children ..." (Insight/Parasoft) > > and...@linux-f29d:~/GROMACS_MD/FZD1> > > Here are MDP files: > > EM.mdp > integrator = steep > nsteps = 200 > nstlist = 10 > rlist = 1.0 > coulombtype = pme > rcoulomb = 1.0 > vdw-type = cut-off > rvdw = 1.0 > nstenergy = 10 > constraints = none > > > integrator = md > nsteps = 2500 > dt = 0.002 > nstlist = 10 > rlist = 1.0 > coulombtype = pme > rcoulomb = 1.0 > vdw-type = cut-off > rvdw = 1.0 > tcoupl = Berendsen > tc-grps = protein non-protein > tau-t = 0.1 0.1 > ref-t = 298 298 > Pcoupl = Berendsen > tau-p = 1.0 > compressibility = 5e-5 5e-5 5e-5 0 0 0 > ref-p = 1.0 > nstenergy = 100 > define = -DPOSRES > > Best regards, > Andrew >> ------------------------------ >> Message: 3 >> Date: Fri, 06 Mar 2009 13:41:28 -0500 >> From: "Justin A. Lemkul" <jalem...@vt.edu> >> Subject: Re: [gmx-users] .gro files problems >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <49b16e58.3000...@vt.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> Andrew Voronkov wrote: >> > Dear GROMACS users, >> > I'm trying to do this tutorial >> > >> It's always best to post a link to the tutorial you're using. There are >> dozens >> of Gromacs tutorials out there. >> > with 1ijy structure from rcsb.org >> > All .gro files on different step raise questions. >> > 1) conf.gro - by VMD I see some strange groups which are not linked with >> > the protein. >> This may or may not be an artefact of VMD's efforts to guess where bonds >> should >> be. Sometimes it's smart, sometimes it's not. >> > 2) After solvatation step in solvated.gro the protein is not in the middle >> > of solution but somewhere in the edge, how to solve this? >> editconf -c >> > 3) After energy minimization protein even goes out of the solution. Looks >> > like I am doing everything according to the tutorial (except the >> > structure) but there are still problems... >> > >> Use editconf -c and try again. >> > The .gro files are in the attachment. >> The listserv ate them, but they probably won't aid much in diagnosis, anyway. >> > On minimization step I also get: >> > Steepest Descents converged to machine precision in 73 steps, >> > but did not reach the requested Fmax >> Depending on what your target Fmax was, this may not be a problem. Fmax < >> 1000 >> is generally adequate for a simple protein in water. >> > On equilibration step I also get an error(with such .gro file it very >> > proabable): >> > >> Or you could have an error in your .mdp file (inappropriate parameters, >> etc), so >> if things continue to fail, post the .mdp file (not as an attachment, just >> embed >> the text). >> -Justin > > > _______________________________________________ > gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
