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Bug #3266

gmx density show wrong symmetrize density profile using -symm?

Added by Super duper about 1 year ago. Updated 11 months ago.

Status:
New
Priority:
High
Assignee:
Super duper
Category:
analysis tools
Target version:
2020.2
Affected version - extra info:
GROMACS - gmx20193d, 2019.3
Affected version:
2019.3
Difficulty:
hard
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Description

Gromacs show wrong symmetrize density profile using -symm while doing gmx density?
In the snapshot, we can see the density profile of the same component with and without -symm
Bilayer simulation using NVE
Volume is constant
gmx20193d density -f traj_comp.xtc -s md.tpr -sl 109 -o density_two.xvg
gmx20193d density -f traj_comp.xtc -s md.tpr -sl 109 -symm -o density_two.xvg
!!!!!

d1.png (9.8 KB) d1.png density profile of membrane Super duper, 12/24/2019 09:59 AM
k.pdf (591 KB) k.pdf system having bilayer Super duper, 12/24/2019 10:00 AM
1.png (421 KB) 1.png Super duper, 12/24/2019 01:46 PM
d.png (7.8 KB) d.png Super duper, 12/24/2019 01:46 PM

History

#1 Updated by Super duper about 1 year ago

Probably this is a problem of Centring based on the center of mass where the layer in the end of z axis

I got correct density after trjconv -trans (translating) trejctory such that it stay around approx center of box
see plot and figure attached

#2 Updated by Paul Bauer 11 months ago

  • Target version changed from 2019.6 to 2020.2

Please upload inputs so we can try to reproduce this and get it fixed.
The fix is going to happen in the 2020 branch though, if this is affected as well

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