[gmx-users] System blowing up - equilibration step - CG simulation
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Mar 6 22:23:51 CET 2015
Hi Carlos,
You can try to contact Floris about the MGDG model.
Cheers,
Tsjerk
On Fri, Mar 6, 2015 at 9:56 PM, Carlos Navarro Retamal <cnavarro at utalca.cl>
wrote:
> Hi Tsjerk,
> I tried to follow as closer as i could the parameters you used, but again
> without luck:
> .mdp file:
> dt = 0.01
> nsteps = 5000000
> nstxout = 0
> nstvout = 0
> nstlog = 10000
> nstxtcout = 1000
> xtc-precision = 10
> rlist = 1.4
> coulombtype = shift
> rcoulomb = 1.2
> epsilon_r = 15
> vdw-type = shift
> rvdw-switch = 0.9
> rvdw = 1.2
> cutoff-scheme = verlet
> tcoupl = Berendsen
> tc-grps = Protein MGDG W_ION
> tau-t = 2.0 2.0 2.0
> ref-t = 323 323 323
> Pcoupl = Berendsen
> Pcoupltype = isotropic
> tau-p = 12.0
> compressibility = 3e-4
> ref-p = 1.0
> refcoord_scaling = com
> (using also -rdd 1.6 and 1.8)
> When i used a timestep of 5fs i was able to run 50ns, but i don’t want to
> cut in half the speed of my simulation since i’m not able to use my GPU's
> (coulomb type and vdw_type = shift).
> What do you suggest me to do?
> Thanks in advance,
>
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>
>
>
> On March 6, 2015 at 5:37:06 PM, Tsjerk Wassenaar (tsjerkw at gmail.com
> <mailto:tsjerkw at gmail.com>) wrote:
>
> Hi Carlos,
>
> Most of that work (and the tutorials) was started some time ago. You can
> use Gromacs 5. At some point, the tutorials will get updated, but usually
> if there's pressure from a course or workshop. Otherwise the science comes
> first :)
>
> Cheers,
>
> Tsjerk
> On Mar 6, 2015 8:38 PM, "Carlos Navarro Retamal" <cnavarro at utalca.cl>
> wrote:
>
> > Hi Tsjerk,
> > Thanks for your kind reply. I just start to reading your manuscript and
> > notice that you used GROMACS version 4.5.5 instead of the latest one
> (5.X)
> > Is there an specific reason to do these? (maybe martini works in a better
> > way with older version of gromacs? )
> > I’m asking you these, because in Martini forums all the tutorial are
> still
> > using gromacs version 4.6.X as the standard.
> > Kind regards,
> > Carlos
> >
> > --
> > Carlos Navarro Retamal
> > Bioinformatics Engineering
> > Ph. D (c) Applied Sciences.
> > Center of Bioinformatics and Molecular Simulations. CBSM
> > University of Talca
> > Av. Lircay S/N, Talca, Chile
> > T: (+56) 712201 798
> > E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
> >
> >
> >
> > On March 6, 2015 at 4:08:21 PM, Tsjerk Wassenaar (tsjerkw at gmail.com
> > <mailto:tsjerkw at gmail.com>) wrote:
> >
> > Hi Carlos,
> >
> > Other things to consider are doing a first short equilibration on a
> single
> > processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd
> > 1.6). Maybe you might want to check the just accepted manuscript on
> > thylakoid membranes from the Martini group (
> > http://dx.doi.org/10.1016/j.bbamem.2015.02.025), which also includes
> MGDG.
> > Those simulations were run with a 10 fs time step.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Fri, Mar 6, 2015 at 7:07 PM, Carlos Navarro Retamal <
> cnavarro at utalca.cl
> > >
> > wrote:
> >
> > > Dear Justin,
> > > I was looking into the paper where the ‘martini’ group described the
> > > parameters for glycolipids, and the mention that in order to
> equilibrate
> > > some glycolipids the had to used a timestep of 5fs. Sadly they not
> > mention
> > > which glycolipid were, so i reduced the timestep from 20fs to 10fs.
> > > I was able to perform performed the equilibration (NPT) with the
> changes
> > > you suggest me (a short one of 5ns).
> > > But later, when i ran the production step of 100ns, at about 60ns the
> > > simulation crashed again (using a timestep of 10fs again).
> > > This is the production .mdp file:
> > >
> > > integrator = md
> > > dt = 0.01
> > > nsteps = 10000000
> > > nstcomm = 10
> > > comm-grps =
> > >
> > > nstxout = 0
> > > nstvout = 0
> > > nstfout = 0
> > > nstlog = 1000
> > > nstenergy = 100
> > > nstxtcout = 1000
> > > xtc_precision = 100
> > > xtc-grps =
> > > energygrps = Protein MGDG W_ION
> > >
> > > nstlist = 10
> > > ns_type = grid
> > > pbc = xyz
> > > rlist = 1.4
> > >
> > > cutoff-scheme = verlet
> > > coulomb-modifier = Potential-shift
> > > vdw-modifier = Potential-shift
> > > epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf =
> > > infinity
> > > verlet-buffer-drift = 0.005
> > >
> > > tcoupl = v-rescale
> > > tc-grps = Protein MGDG W_ION
> > > tau_t = 1.0 1.0 1.0
> > > ref_t = 320 320 320
> > > Pcoupl = parrinello-rahman
> > > Pcoupltype = semiisotropic
> > > tau_p = 12.0 12.0 ;parrinello-rahman is more stable
> > > with larger tau-p, DdJ, 20130422
> > > compressibility = 3e-4 3e-4
> > > ref_p = 1.0 1.0
> > >
> > > gen_vel = no
> > > gen_temp = 320
> > > gen_seed = 473529
> > >
> > > constraints = none
> > > constraint_algorithm = Lincs
> > > unconstrained_start = no
> > > lincs_order = 4
> > > lincs_warnangle = 30
> > > I’m currently increasing the time of equilibration step to 50ns.
> > > What else do you suggest me?
> > > Best regards,
> > > Carlos
> > > --
> > > Carlos Navarro Retamal
> > > Bioinformatics Engineering
> > > Ph. D (c) Applied Sciences.
> > > Center of Bioinformatics and Molecular Simulations. CBSM
> > > University of Talca
> > > Av. Lircay S/N, Talca, Chile
> > > T: (+56) 712201 798
> > > E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
> > >
> > >
> > >
> > > On March 6, 2015 at 12:26:28 PM, Carlos Navarro Retamal (
> > > cnavarro at utalca.cl<mailto:cnavarro at utalca.cl>) wrote:
> > >
> > > Dear Justin,
> > > Thanks for your kind reply.
> > > Is there a way to set up a bilayer membrane system without a protein
> > using
> > > insane? I’ve already several CG simulations with this protein, so i'm
> > > pretty sure that its parameters are ok. I do have some issues with the
> > > glycolipid used (MGDG) This is the first time i used the parameters
> > gotten
> > > from
> > >
> >
> http://md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0_glycolipids.itp
> > > so i don’t know if this kind of molecules requieres an specific
> > > temperature (for example)
> > > Best regards,
> > > Carlos
> > > --
> > > Carlos Navarro Retamal
> > > Bioinformatics Engineering
> > > Ph. D (c) Applied Sciences.
> > > Center of Bioinformatics and Molecular Simulations. CBSM
> > > University of Talca
> > > Av. Lircay S/N, Talca, Chile
> > > T: (+56) 712201 798
> > > E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
> > >
> > >
> > >
> > > On March 6, 2015 at 11:56:01 AM, Justin Lemkul (jalemkul at vt.edu
> <mailto:
> > > jalemkul at vt.edu>) wrote:
> > >
> > >
> > > On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:
> > > > Dear Gromacs users,
> > > > I'm trying to perform a CG simulations of a system consisting in a
> > > protein locate at 5 nm with respect to the charged groups of a MGDG
> > > membrane.
> > > > I first performed an EM in vaccum.
> > > > After that, to constructed the system i use insane.py as following:
> > > > ./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm
> 5
> > > -box 10,10,10 -l MGDG -sol W -orient
> > > >
> > > > Later, i ran a EM with the whole system, with the respective output:
> > > > Steepest Descents converged to machine precision in 2081 steps,
> > > > but did not reach the requested Fmax < 10.
> > > > Potential Energy = -2.6833109e+05
> > > > Maximum force = 3.5193942e+02 on atom 3598
> > > > Norm of force = 6.2432761e+00,
> > > >
> > > > Sadly, when i'm trying to perform an equilibration i got the
> following
> > > error message:
> > > > Step 10:
> > > > Atom 8449 moved more than the distance allowed by the domain
> > > decomposition (1.590000) in direction Z
> > > > distance out of cell 1330.886108
> > > > Old coordinates: 1.667 4.809 0.710
> > > > New coordinates: -1840.027 -454.814 1335.667
> > > > Old cell boundaries in direction Z: 0.000 5.000
> > > > New cell boundaries in direction Z: 0.000 4.781
> > > > ________________________________
> > > > Program mdrun, VERSION 5.0.4
> > > > Source code file:
> > > /home/krlitros87/Downloads/gromacs-5.0.4/src/gromacs/mdlib/domdec.c,
> > line:
> > > 4390
> > > >
> > > > Fatal error:
> > > > An atom moved too far between two domain decomposition steps
> > > > This usually means that your system is not well equilibrated
> > > > For more information and tips for troubleshooting, please check the
> > > GROMACS
> > > > website at www.gromacs.org/Documentation/Errors<
> > > http://www.gromacs.org/Documentation/Errors>
> > > >
> > > >
> > > > This is the .mdp file:
> > > > define = -DPOSRES
> > > > dt = 0.02
> > > > cutoff-scheme = group
> > > > nsteps = 500000
> > > > nstxout = 0
> > > > nstvout = 0
> > > > nstlog = 100
> > > > nstxtcout = 100
> > > > xtc-precision = 10
> > >
> > > Any reason to sacrifice so much precision? Maybe for a CG system it
> > doesn't
> > > matter so much.
> > >
> > > > rlist = 1.4
> > > > coulombtype = shift
> > > > rcoulomb = 1.2
> > > > epsilon_r = 15
> > > > vdw-type = shift
> > > > rvdw-switch = 0.9
> > > > rvdw = 1.2
> > > > tcoupl = Berendsen
> > > > tc-grps = Protein MGDG W ION
> > >
> > > Coupling water and ions separately is generally unstable.
> > >
> > > > tau-t = 1.0 1.0 1.0 1.0
> > > > ref-t = 323 323 323 323
> > > > Pcoupl = Berendsen
> > >
> > > If NPT is failing, reduce complexity and start by equilibrating with
> NVT.
> > >
> > > > Pcoupltype = isotropic
> > > > tau-p = 5.0
> > > > compressibility = 3e-4
> > > > ref-p = 1.0
> > > > refcoord_scaling = all
> > >
> > > Try refcoord-scaling = com; the all option can be unstable.
> > >
> > > >
> > > > I know that my system is blowing up, but what can i do to avoid this
> > > issue? I tried increasing the EM step without luck.
> > >
> > > What about all the rest of the advice at
> > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up? Your EM
> > seems
> > > fine, so I doubt that's it. Something is either unstable in the
> topology
> > > or the
> > > dynamics. Split the system into parts to make sure you can stably
> > simulate
> > > everything - protein in water, membrane alone, etc.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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