Thanks for the suggestions. I can see how a smaller dt would probably be the most general approach to use as it should work with just about any reasonable combination of settings.
-- Josh On Tue, 2011-05-31 at 11:02 +1000, Mark Abraham wrote: > On 31/05/2011 10:54 AM, Justin A. Lemkul wrote: > > > > > > Joshua L. Phillips wrote: > >> I've found that I often get LINCS warnings like this when starting from > >> highly extended conformations when using implicit solvent. The GBSA > >> surface tension combined with the lack of viscosity (due to the absence > >> of explicit water) allows the protein to change conformation much faster > >> than LINCS likes by default. > >> > >> Normally, I just run a short vacuum simulation (keep the same settings > >> as Justin suggested but set GBSA = No) to let the system relax a little > >> more before starting a GBSA run (EM is often just not enough). Usually > >> only about 50ps. Also, doing this with position restraints can help slow > >> down the collapse, and usually results in just enough collapse that the > >> following GBSA run will satisfy the default LINCS settings. > >> > >> Another option might be to run a short simulation with GBSA turned on, > >> but using Langevin dynamics to include some additional friction that > >> should slow down the initial collapse. > >> > > > > That's generally a good idea. We often use the sd integrator when > > doing GBSA calculations. > > > >> Also, you could fudge with the environment variables associated with > >> LINCS, but this seems a little dangerous compared to the above two > >> suggestions. > >> > > > > I wouldn't say "a little dangerous," I'd say "very dangerous" :) If > > the constraints are failing, it's not necessarily (or usually) their > > fault. The system is unstable, and trying to just override this will > > give you a trajectory, but you should be concerned that this > > trajectory is being ruled by spurious forces. > > > >> I would be interested in peoples' opinions and suggestions on how to > >> handle this issue as it is quite common when starting from highly > >> extended structures using GBSA. Some proteins are more susceptible than > >> others... > >> > > > > Reducing the timestep is a good option. If the dynamics are occurring > > so fast that the constraints can't keep up, reducing dt can help. > > Agreed. Even using all-vs-all kernels, I've observed similar symptoms as > the OP lately with excessive rotation of v-site terminal methyl groups. > I can generate stable trajectories by starting my equilibration with 0.5 > fs timesteps, and switching later. > > Mark > > > > > -Justin > > > >> I also tend to find that version 4.5.4 is much more stable than even > >> 4.5.3 for implicit solvent simulations. > >> > >> -- Josh > >> > >> On Mon, 2011-05-30 at 18:06 -0500, Michael D. Daily wrote: > >>> Thanks Justin, this is very helpful. I'll attempt these fixes > >>> tomorrow. > >>> > >>> Mike > >>> > >>> On 5/30/2011 5:50 PM, Justin A. Lemkul wrote: > >>>> > >>>> Michael D. Daily wrote: > >>>>> Hi all, > >>>>> > >>>>> I'm trying to run implicit solvent calculations in gromacs 4.5 > >>>>> with the charmm forcefield. I am able to minimize successfully > >>>>> and compile for > >>>> When troubleshooting, it is always advisable to try the latest > >>>> version (4.5.4) to see if the problem is reproducible. If a > >>>> pertinent bug has been fixed, there's no use troubleshooting the > >>>> broken version. > >>>> > >>>>> mdrun, but soon after starting, mdrun complains about excessive > >>>>> rotation in LINCS (see the error printed below that). I also > >>>>> include my mdp file at the bottom. Can anyone advise me as to the > >>>>> possible cause of such errors, as it is difficult to diagnose > >>>>> given that grompp worked fine. > >>>>> > >>>> For reference: > >>>> > >>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > >>>> > >>>> > >>>> > >>>> If grompp worked, that just means your coordinate and topology > >>>> matched and there were no internal conflicts within the .mdp file. > >>>> It is no guarantee that the resulting simulation will actually > >>>> work, unfortunately. > >>>> > >>>>> --- lincs error --- > >>>>> > >>>>> Step 1, time 0.002 (ps) LINCS WARNING > >>>> Typically an instant LINCS failure indicates insufficient > >>>> minimization. You said you minimized successfully, but what does > >>>> this mean? What values did you achieve for Fmax and Epot? > >>>> > >>>>> relative constraint deviation after LINCS: > >>>>> rms 0.000780, max 0.020692 (between atoms 880 and 881) > >>>>> bonds that rotated more than 30 degrees: > >>>>> atom 1 atom 2 angle previous, current, constraint length > >>>>> 606 607 36.7 1.0527 0.1080 0.1080 > >>>>> 614 615 35.6 0.8972 0.1125 0.1111 > >>>>> 614 616 75.3 0.1054 0.1121 0.1111 > >>>>> 880 881 58.0 0.1068 0.1134 0.1111 > >>>>> 880 882 50.4 0.9168 0.1121 0.1111 > >>>>> 889 890 55.3 0.1066 0.1122 0.1111 > >>>>> 889 891 35.3 0.8588 0.1118 0.1111 > >>>>> > >>>>> ---- mdp file ------------ > >>>>> > >>>>> ; title and include files > >>>>> title = 1EX6-S35P_md1 > >>>>> cpp = cpp > >>>>> include = > >>>>> -I/home/yoo2/myusr/gromacs-3.3.3/share/gromacs/top/ -I./ > >>>> Any reason you're including files from an ancient Gromacs version? > >>>> > >>>>> define = > >>>>> ; integrator and input/output setting up > >>>>> integrator = md > >>>>> nsteps = 1000000 ; 2 ns > >>>>> ;nsteps = 5000 ; 2 ns > >>>>> dt = 0.002 > >>>>> nstxout = 5000 > >>>>> nstvout = 5000 > >>>>> nstenergy = 500 > >>>>> nstxtcout = 500 > >>>>> nstlog = 500 > >>>>> xtc_grps = System > >>>>> energygrps = System > >>>>> comm_mode = Linear > >>>>> > >>>>> ;implicit solvent > >>>>> implicit_solvent = GBSA > >>>>> gb_algorithm = Still > >>>>> gb_saltconc = 0.15 > >>>> FYI, gb_saltconc is nonfunctional. Don't expect it to do anything :) > >>>> > >>>>> rgbradii = 1.0 > >>>>> > >>>>> ; neighbor searching and vdw/pme setting up > >>>>> nstlist = 10 > >>>>> ns_type = grid > >>>>> pbc = xyz > >>>>> ;rlist = 1.4 > >>>>> rlist = 1.0 > >>>>> > >>>>> ;coulombtype = pme > >>>>> coulombtype = Cut-Off > >>>>> fourierspacing = 0.1 > >>>>> pme_order = 6 > >>>>> ;rcoulomb = 1.4 > >>>>> rcoulomb = 1.1 > >>>>> > >>>>> ;vdwtype = switch > >>>>> vdwtype = Cut-Off > >>>>> rvdw_switch = 1.0 > >>>>> ;rvdw = 1.2 > >>>>> rvdw = 1.1 > >>>>> > >>>> All of these are potentially problematic. Running implicit > >>>> simulations typically requires longer cutoffs than would normally > >>>> be needed for explicit solvent simulations. Try > >>>> rlist=rvdw=rcoulomb=2.0 nm. > >>>> > >>>>> ; cpt control > >>>>> tcoupl = nose-hoover > >>>> A better choice for initial equilibration would be either V-rescale > >>>> or Berendsen. I know this can be an issue in explicit solvent, > >>>> when velocities can oscillate a lot at the outset of a simulation > >>>> using Nose-Hoover and the simulation box can explode; I don't know > >>>> if this is such a big deal with implicit, but it can't hurt to try. > >>>> > >>>>> tc-grps = System > >>>>> tau_t = 0.4 > >>>>> ref_t = 300.0 > >>>>> Pcoupl = parrinello-rahman > >>>> I don't know how an implicit box will respond to pressure coupling, > >>>> but it would be better to try NVT first and see if it's stable, > >>>> then try NPT and see if things break down. > >>>> > >>>> One option that might be advantageous is to use the all-vs-all > >>>> kernels for a speed upgrade. You can accomplish this with: > >>>> > >>>> rlist = 0 > >>>> nstlist = 0 > >>>> rvdw = 0 > >>>> rcoulomb = 0 > >>>> rgbradii = 0 > >>>> pbc = no > >>>> comm-mode = angular > >>>> > >>>> You'd have to run with mdrun -pd (particle decomposition), but the > >>>> end result can be quite fast and you avoid potential periodicity > >>>> effects. > >>>> > >>>> -Justin > >>>> > >>> > >>> -- > >>> Michael D. Daily, Ph.D. > >>> Postdoctoral Fellow > >>> Qiang Cui group > >>> Department of Chemistry > >>> University of Wisconsin-Madison > >>> > >> > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Joshua L. Phillips Ph.D. Candidate - School of Engineering University of California, Merced jphilli...@ucmerced.edu -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
