[gmx-users] System blowing up - equilibration step - CG simulation

Fri Mar 6 20:37:48 CET 2015

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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