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Bug #3266

gmx density show wrong symmetrize density profile using -symm?

Added by Super duper 2 months ago. Updated 2 months ago.

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

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 2 months 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

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