[gmx-users] no domain decomposition

[Tsjerk Wassenaar]

Hi Soumadwip,

Are you sure you have the order of molecules the same in the starting
structure and the topology? If you have, and you're confident everything
should be fine, then run the energy minimization writing out each frame.
That should show you where the action is happening and allow zooming in on
it. Doing NVT at very low temperature is cool too for diagnostics :)

Cheers,

Tsjerk


On Thu, Sep 24, 2015 at 7:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/24/15 1:19 PM, soumadwip ghosh wrote:
>
>> Hi Mark and Justin,
>>             actually I have simulated each item with pure SPCE water
>> separately for a few nanoseconds and they are absolutely fine. The
>> initial structure ( a small dna inside a CNT) was generated using
>> Packmol and may be due to this I have this error occuring each time.
>> Justin asked me to carefully look into the nvt.log file which I have
>> attached in my previous mail. But I am unable to detect any source of
>>
>
> The list does not accept attachments.  One of us says that every day...
>
> that error from it. Tsjerk suggested that for my system -nt has to be
>> kept less than 8. I tried that too but the same LINCS warning pops up.
>> My question is is there any way to fix the problem using some options
>> in the mdrun prompt? I  think I have correct topologies since I am
>>
>
> You should upload your .log file and any pertinent .mdp file(s) and
> provide links.
>
> able to simulate each species separately. Hence, technically is there
>> a viable solution? Like I can tell you I deliberately kept the box
>> size 1000 nm3 to replicate some observations while the use of editconf
>> sugeested the box size should be 580 nm3 but can this be the issue? At
>>
>
> editconf does what it's told; I don't know how it can "suggest" anything.
> Without the exact sequence of commands of what you did, this description is
> really not useful.
>
> -Justin
>
> this point I am thinking of repeating the simulation keeping a small
>> box in mind. However, it would be really helpful if someone can
>> provide some insights in fixing this problem .
>>
>> Regards,
>> Soumadwip
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Tsjerk A. Wassenaar, Ph.D.