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.war...@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 <jalem...@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.war...@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.war...@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.war...@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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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