Plotting Protein Distance from Membrane over time

User discussions
1

GROMACS version:
GROMACS modification: Yes/No

Hello, I’m trying to plot the distance of a protein from a phopholipid layer. I am trying to use this command in my jupyter notebook:

!gmx distance -f hvr060-040_pub.xtc -s hvr060-040_pub.gro -oav distave.xvg -select “Protein” “POPC”
!xmgrace distace.xvg

but I’m having trouble installing grace / xmgrace using conda.

conda install -c uvcdat xmgrace

Results in compatibility issues (see below), requiring python2.7 or lower. Do people not use xmgrace as much anymore? Are there any other versions or software that can be used instead?

Could not solve for environment specs
The following packages are incompatible
├─ pin-1 is installable and it requires
│ └─ python 3.12.* , which can be installed;
└─ xmgrace is not installable because it requires
└─ python [2.7* |>=2.7,<2.8.0a0 ] but there are no viable options
├─ python [2.7.12|2.7.13|…|2.7.18] conflicts with any installable versio ns previously reported;
└─ python 2.7.15 would require
└─ openssl >=1.1.1,<1.1.2.0a0 , which does not exist (perhaps a missing channel).

2

.xvg files can be read like a .txt file, you can use numpy.loadtxt(filename,comments=[“@”, “#”],unpack=True) to read the file and matplotlib to plot it.

Regarding the issue of installing xmgrace with conda, I personally have never been able to get it to work on mac so can’t really help with that