[gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

[Justin Lemkul]

On 9/27/17 7:54 PM, Dallas Warren wrote:
> Left the 37 one running, and it ended up being "Killed". Was
> distracted, so didn't really see how long it ran etc, but suspect it
> was due to amount of memory being used up.
> 
> I am going about this the right way? i.e. want the RDF between atoms
> at either end of the molecule (38 atoms long), and don't want the
> atoms within the same molecule included in the calculation then need
> to set nrexcl to 37?

I'm assuming you're trying to get the RDF simply by selecting the whole 
molecule? Why not just use index groups with the starting and ending atoms in 
separate groups and compute the RDF of one around the other?

-Justin

> Catch ya,
> 
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
> 
> 
> On 28 September 2017 at 09:02, Dallas Warren <dallas.warren at monash.edu> wrote:
>> Just want to check that this should be taking as long as it is
>> (expected behaviour etc), for grompp to generate the tpr when nrexcl
>> is large.
>>
>> I have a long straight chain molecule with 38 atoms that are
>> generating RDFs for, so need to change the [ moleculetype ] nrexcl to
>> exclude atoms within the same molecule from the generated RDFs.
>> Initially set nrexcl to 37, ran grompp to get the tpr, and it was
>> taking a loooong time and consuming significant amounts of memory.
>> Killed it and ran a few tests with increasing values and it is pretty
>> much instantaneous up until about 25.  Each increase after that
>> increases the time it takes in the " excluding ## bonded neighbours
>> molecule type '####' " step.
>>
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.warren at monash.edu
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble a nail.

-- 
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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