Segmentation faulty inquiry?

User discussions
1

Hello I am trying the below command within Tutorial2 (Membrane):

gmx genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000

and am getting:

Reading structure file
Select group to position restrain
zsh: segmentation fault /opt/gromacs2020-2/bin/gmx_d genrestr -f KALP_newbox.gro -o strong_posre.itp

what in particular should I amend?

Thanks:)

2

This is a known bug (posted many times to this forum - please search before posting!) that was fixed in version 2020.3. Upgrade and try again.

3

Hello and thank you for your kind update,

I will search first.

Much Thanks:)

4

Hello Justin,

as recommended I upgraded to 2020.3 via:

  1. Open iTerm

  2. Type “brew upgrade”

  3. Then type “brew install gromacs”

, however, am struggling with which gromacs command to open this newest version i.e. when i use my old command: /opt/gromacs2020-2/bin/gmx_d -h my older version 2020.2 opens. I understand that this is something more technical that you may be not able to answer unless getting into my iTerm however if it something simple feel free to comment, thanks:): I searched the forum and tried for a while on my own with no solution as well accordingly will just end up vending outside help if I must.

Much Thanks and I did not post a fresh inquiry since I believe this inquiry may be outside of your forum:)

5

I have no experience installing GROMACS through HomeBrow or in using iTerm, but certainly if you are calling /opt/gromacs2020-2/bin/gmx_d then you’re going to get a 2020.2 version because you’re asking your terminal to use it.

6

Hello and thank you for your kind update and yes I juggled that input around quite a bit (2020-3 etc.) with no success. I will keep working on it👍.