[gmx-users] MARTINI crushing

[James Starlight]

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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