[gmx-users] implicit solvent LINCS errors
Joshua L. Phillips
jphillips7 at ucmerced.edu
Wed Jun 1 01:08:29 CEST 2011
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
> >>>
> >>
> >
>
> --
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--
Joshua L. Phillips
Ph.D. Candidate - School of Engineering
University of California, Merced
jphillips7 at ucmerced.edu
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