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" <[email protected]> > Subject: Re: [gmx-users] .gro files problems > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
