Oh I see this tutorial solvates before minimization. I'm heading out, but I'll give it a go tonight.
On Mon, Mar 9, 2009 at 3:57 PM, Jack Shultz <[email protected]> wrote: > 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 <[email protected]> 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" <[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 >> > > > > -- > Jack > > http://www.facebook.com/home.php#/profile.php?id=832713248 > http://hydrogenathome.org > -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org _______________________________________________ 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
