[gmx-users] MARTINI crushing

Thu Apr 14 15:53:16 CEST 2016

Hmm.. Martini proteins should run fine with ~30fs timesteps. Could you
check the bonded parameters for the bond listed, and take this to the
Martini forum (cgmartini.nl)?
@Mark: The Martini forcefield was validated with timesteps between 10 and
40 fs; although some of the parametrised molecules (such as DNA) only work
with the smaller timesteps.

Peter

On Thu, Apr 14, 2016 at 3:47 PM, James Starlight <jmsstarlight at gmail.com>
wrote:

> actually I have the same system with the same mdp options simulated in
> parallel where I dont have such warnings.  so I dont know the sourse
> of that error in the latter case
>
> the only different between two was t_coupling used in equilibration (0.5
> vs 1.0)
>
> 2016-04-14 15:34 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> > Hi,
> >
> > That depends. Why do you think the increase in integration step is a
> valid
> > model physics?
> >
> > Mark
> >
> > On Thu, Apr 14, 2016 at 3:25 PM James Starlight <jmsstarlight at gmail.com>
> > wrote:
> >
> >> another problem when I try to increase slightly integration step from
> >> 0.01 to 0.02 I obtain
> >>
> >> WARNING 1 [file system.top, line 44]:
> >>   The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an
> >>   estimated oscillational period of 9.7e-02 ps, which is less than 5
> times
> >>   the time step of 2.0e-02 ps.
> >>   Maybe you forgot to change the constraints mdp option.
> >>
> >> that is waht related to constraints in my mdp
> >> constraints              = none
> >> constraint_algorithm     = Lincs
> >> unconstrained_start      = no
> >> lincs_order              = 2
> >> lincs_warnangle          = 30
> >>
> >> Can I ignore this warning?
> >>
> >> J.
> >>
> >> 2016-04-14 10:05 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> >> > passing -rdd with a larger value forces mdrun to make larger domain
> >> cells,
> >> > basically reducing the number of ranks you can use and hampering
> >> > parallelization. I don't think it affects the physics.
> >> > Reducing the CPU count does the same thing.
> >> >
> >> > Peter
> >> >
> >> > On Thu, Apr 14, 2016 at 9:57 AM, James Starlight <
> jmsstarlight at gmail.com
> >> >
> >> > wrote:
> >> >
> >> >> an question: might the bigger -rdd like 1.8 or 2.0  produce ssmth bad
> >> >> in simulation? generally I found that with rdd 1.8 the siduation is
> >> >> better, also I reduced number of CPU for that job from 256 to 128 and
> >> >> it works OK by now!
> >> >>
> >> >> Gleb
> >> >>
> >> >> 2016-04-14 9:40 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> >> >> > Hi James,
> >> >> >
> >> >> > 1) use a newer version of Gromacs
> >> >> > 2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn
> >> are so
> >> >> > long and flexible they occasionally confuse gromacs' domain
> >> >> decomposition.
> >> >> >
> >> >> > Peter
> >> >> >
> >> >> > On Thu, Apr 14, 2016 at 8:49 AM, James Starlight <
> >> jmsstarlight at gmail.com
> >> >> >
> >> >> > wrote:
> >> >> >
> >> >> >> Dear Gromacs Users!
> >> >> >>
> >> >> >> I faced with the problems while simulating of big MARTINI system
> of
> >> >> >> membrane protein complex within big membrane consisted totally of
> 55k
> >> >> >> martini CG atoms.
> >> >> >>
> >> >> >> On the early stage of the NPT equilibration I have a error
> >> >> >>
> >> >> >> Program g_mdrun_openmpi, VERSION 4.5.7
> >> >> >> Source code file:
> >> >> >> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_top.c, line:
> 173
> >> >> >>
> >> >> >> Software inconsistency error:
> >> >> >> Some interactions seem to be assigned multiple times
> >> >> >> For more information and tips for troubleshooting, please check
> the
> >> >> GROMACS
> >> >> >> website at http://www.gromacs.org/Documentation/Errors
> >> >> >> -------------------------------------------------------
> >> >> >>
> >> >> >>
> >> >> >> does the problem is related to paralelization or smth wrong with
> >> >> >> setup? Amazing that on the same system without Elnedyn applied I
> have
> >> >> >> no such promlems at ell.
> >> >> >>
> >> >> >> Thanks so much for help!
> >> >> >>
> >> >> >> J.
> >> >> >> --
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