[gmx-users] System blowing up - equilibration step - CG simulation
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Mar 6 20:19:18 CET 2015
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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