Dear Christian, > mmh, just my 0.02€: I guess in a very rough energy landscape (as in > solvated peptides or proteins) this is not generally true, because > with small steps the system might get stuck in the next tiny local > minimum, while with a larger step size it may jump across it. > And I guess exactly this happens in your failing simulations: Your > system is stuck in a local minimum high up on the slopes of the energy > funnel. I guess this is just normal and happens some times. You might > alter the system by a little modeling (move the problematic atoms > slightly), or try -DFLEXIBLE, or perhaps rather increase step size. > Double precision minimization has proved to be more stable for me in > problematic cases, like straightening out a skewed average structure > of a trajectory.
If the system is truly in a local minimum, the force should be small, right, since the force is by definition zero at any minimum (local or otherwise)? I agree there may be situations in which the *energy* may still be very unfavorable after minimization, but the forces should be small. I should note that I never have these problems (incomplete minimization) with any other simulation package I use, so I strongly suspect that the problem is something that GROMACS in particular is doing in minimization, and *not* just a general problem with minimizing on a high-dimensional landscape. David > Regards > > Christian > > > > > > Thanks, > > David > > > > > >> Best > >> XAvier > >> > >> > >> > >> > I often have problems with minimization in gromacs, but now I think I > >> > have something a little more systematic to say. > >> > > >> >First, my system: I am simulating a short peptide in a mix of two > >> > co-solvents. I use a program called packmol which can start pack > >> > specified number of molecules into a box of specified size, with a > >> > specified distance tolerance between atoms, to generate starting gro > >> > files. I am simulating a number of variants of this peptide in various > >> > mixes of the two co-solvents (one of which is water). > >> > > >> > The problem I am having is that, even in double precision, gromacs > >> > fails to properly minimize some of the systems -- minimization using > >> > any of the minimizers I've tried (including steepest descents, my > >> > preference) often terminates early (i.e. after ~50 steps) even in > >> > double precision, leaving really large forces on some of the atoms > >> > (usually 10^10 or more). The largest forces are usually on one atom of > >> > a water molecule. Hence, when I plug the minimized output into > >> > equilibration, my simulations explode due to large forces. > >> > > >> > Small tweaks to the system can change whether minimization works > >> > properly or not in some cases -- for example, switching from double > >> > precision to single precision will make some systems which fail in > >> > double minimize properly, as will changing cutoffs. I assume also > >> > things like changing architectures will allow some systems to minimize > >> > (I've seen this behavior in the past). > >> > > >> > The problem is, I can find no combination of settings which will allow > >> > *all* of my systems to minimize properly. Inevitably some fail, and I > >> > end up having to go in by hand, look at the minimization log file, see > >> > which water molecule has the huge force on it, and tweak its position > >> > slightly by hand in the input gro file. Typically then minimization > >> > will proceed just fine. > >> > > >> > This brings me to my question: Are the minimization algorithms > >> > truncating some of the forces at some threshold value or something? > >> > That is, why does minimization often end even though forces are still > >> > huge? > >> > > >> > Currently, I'm using steepest descents with constraints turned off, > >> > double precision, and emstep = 1.0e-8. I'm using Gromacs 3.3.2, rlist > >> > = 0.9 = rcoulomb, rvdw-switch = 0.75 and rvdw = 0.8, pme_order 4, > >> > ewald_rtol = 1e-04, and fourierspacing = 0.12, DispCorr = AllEnerPres, > >> > and switched vdw. > >> > > >> > Any tips will be appreciated. Having to tweak coordinates by hand (or > >> > write a script to do it) to get things to minimize isn't really a > >> > satisfactory solution for me. > >> > > >> > I could submit a bugzilla, but I imagine what will happen if I submit > >> > the cases that don't work for me is that they'll work fine for whoever > >> > addresses the bugzilla and so this won't be regarded as a real > >> > problem. Alternatively I could submit a whole slate of starting system > >> > configurations and someone can debug just the ones that fail for them. > >> > > >> > Thanks, > >> > David > >> > _______________________________________________ > >> > 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 [EMAIL PROTECTED] > >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> ----------------------------------------------------- > >> XAvier Periole - PhD > >> > >> NMR & Molecular Dynamics Group > >> University of Groningen > >> The Netherlands > >> http://md.chem.rug.nl/~periole > >> ----------------------------------------------------- > >> _______________________________________________ > >> 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 [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > _______________________________________________ > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php