[gmx-users] System blowing up - equilibration step - CG simulation
Carlos Navarro Retamal
cnavarro at utalca.cl
Fri Mar 6 19:19:52 CET 2015
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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