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

[Justin Lemkul]

On 9/28/17 12:25 AM, Dallas Warren wrote:
> Justin,
>
> No, I have separate index groups for each of the atom types.
>
> Wouldn't that still have the pair of atoms that are located on the
> same molecule, contributing to the RDF?
>
> Molecule is like this:
> C1 -------C38
>
> Index file would be something like this:
> [ C1 ]
> 1 39 77 .....
>
> [ C38 ]
> 38 76 114 ....
>
> So doesn't it still include these atom pairs to generate the RDF? Atom
> pair list below.  From the RDFs that are generating using this method,
> it appears it does as there is a massive peak around the intra-atomic
> distance.
>
> 1-38, 1-76, 1-114 ..... 39-38, 39-76, 39-114 ....
>
> First and fifth pair in this list are atoms that are contained within
> the same molecule.
>
> Wouldn't be surprised if I am missing something simple here .....

No, I misunderstood what you were actually after. What you are asking 
for does require a huge intramolecular nrexcl and you are indeed 
seemingly running out of memory trying to create such a huge exclusion 
list. Sorry to say I don't have much more to suggest here.

-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 10:27, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>> 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.
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================