[gmx-users] MARTINI crushing

[James Starlight]

yep the problem is a really strange because there is no different
between mdp options

the only thing is in first case I dont apply elnedyn on the protein
and and the second one (where the warning has appeared) I do !

Hovewer I didnt find on martini tutorials that elnedyns should produce
any difference between mdps used for the simulation compared
unresstrained runs


2016-04-14 15:53 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> 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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