[gmx-users] MARTINI crushing

[Mark Abraham]

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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