[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Antara mazumdar]

Dear Sir,

I have used 1.8 rdd value.

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Sat, May 14, 2016 at 12:14 AM, subhadip das <das.subhadip64 at gmail.com>
wrote:

> Can you tell me of the constraint parameter u used and the corresponding
> atom names
> On 14 May 2016 00:11, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:
>
>> Hi Antara,
>>
>> What commands did you use? At least make sure you add -rdd 1.6 to the
>> command line of mdrun, because the default value is too small for coarse
>> grain simulations.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar <antara.mazumdar at igib.in
>> >
>>
>> wrote:
>>
>> > Dear users,
>> >
>> > I am trying to run a coarse grained simulation of a membrane protein in
>> a
>> > mixed lipid billayer using martini model 2.2. I have already performed
>> all
>> > the equilibration steps successfully on my desktop with GROMACS 5.1.0.
>> > However, when i try to execute its production run in parallel(having
>> > gromacs 5.1 version installed)  it complains of LINCS warning and
>> > terminates at step 0. But on the contrary, it runs on the desktop
>> > successfully. Kindly suggest something and please let me know if any
>> more
>> > information is required from my side.
>> >
>> >
>> > Thanks!!
>> >
>> > Kind Regards,
>> > Antara
>> >
>> > --
>> > Junior research fellow(project)
>> > Systems biology group
>> > CSIR-Institute of Genomics & Integrative Biology
>> > South Campus
>> > New Delhi -  110020
>> > M : +91-9717970040
>> > --
>> >
>> >
>> >
>> > On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar <
>> antara.mazumdar at igib.in
>> > >
>> > wrote:
>> >
>> > > Dear gromacs users,
>> > >
>> > > I am trying to run a coarse grained simulation of a membrane protein
>> in a
>> > > mixed lipid billayer using martini model. I have already performed all
>> > the
>> > > equilibration steps successfully on my desktop. However, when i try to
>> > > execute its production run in parallel it complains of LINCS warning
>> and
>> > > terminates at step 0. But on the contrary, it runs on the desktop
>> > > successfully. Kindly suggest something and please let me know if any
>> more
>> > > information is required from my side.
>> > >
>> > >
>> > > Thanks!!
>> > >
>> > >
>> > >
>> > > Kind Regards,
>> > > Antara
>> > >
>> > > --
>> > > Junior research fellow(project)
>> > > Systems biology group
>> > > CSIR-Institute of Genomics & Integrative Biology
>> > > South Campus
>> > > New Delhi -  110020
>> > > M : +91-9717970040
>> > > --
>> > >
>> > >
>> > >
>> > --
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> --
>> Gromacs Users mailing list
>>
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>