Discussion:
Strange behavior of water droplet on a solid surface with Verlet cutoff scheme in GMX 5.0.4
(too old to reply)
Jan Jirsák
2015-06-30 09:34:45 UTC
Permalink
Dear community,

I simulate a droplet made of rigid SPC waters (ca 10000 molecules)
lying on a solid surface placed at z=0 represented by LJ atoms with
fixed coordinates. Using cutoff-sheme = Verlet with quite long cutoff
(3.0nm) produces a strange spurious force, which seems to pull the
droplet towards the origin (or maybe in the -1,-1,0 direction). It is
not caused by particular configuration, because even when I rotate the
setup by 180 deg., the strange force still pulls the droplet in the
same direction - to the origin, i.e. in the opposite direction
relative to the configuration.

When I decrease the cutoff to, say, 1.9 nm or when I use a group
scheme instead, the artifact disappears.

Does anybody have a clue what could be happening? Does anybody observe
anything similar?

With kind regards,
Jan
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Mark Abraham
2015-06-30 20:55:53 UTC
Permalink
Hi,

If there was an empty domain, that might cause artefacts if you ran with
GPUs. Fixed in 5.0.5

Mark
Post by Jan Jirsák
Dear community,
I simulate a droplet made of rigid SPC waters (ca 10000 molecules)
lying on a solid surface placed at z=0 represented by LJ atoms with
fixed coordinates. Using cutoff-sheme = Verlet with quite long cutoff
(3.0nm) produces a strange spurious force, which seems to pull the
droplet towards the origin (or maybe in the -1,-1,0 direction). It is
not caused by particular configuration, because even when I rotate the
setup by 180 deg., the strange force still pulls the droplet in the
same direction - to the origin, i.e. in the opposite direction
relative to the configuration.
When I decrease the cutoff to, say, 1.9 nm or when I use a group
scheme instead, the artifact disappears.
Does anybody have a clue what could be happening? Does anybody observe
anything similar?
With kind regards,
Jan
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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