Regarding calculating water orientational relaxation

[Lee YeongKyu]

Dear Users,

Hello. I am new to MDanalysis. I need to calculate the WOR for the bulk water system ( system just containing water molecules). I have read manual explaining how to use WOR but I am not sure how to use that. 

1. Is it fine to use Universe(gro, trajectory) where the trajectory is in the format of gro?

2. In the select line, I am totally lost. I want to reproduce the data generated by the reference in the manual regarding the WOR. But I am confused of which word should I use.

Can anyone help me to figure it out?

Thanks in advance and with my best regards

[Oliver Beckstein]

Hi Lee YeongKyu,

Welcome to the mailing list!

On Dec 22, 2021, at 6:21 PM, Lee YeongKyu <monste...@gmail.com> wrote:

Dear Users,

Hello. I am new to MDanalysis. I need to calculate the WOR for the bulk water system ( system just containing water molecules). I have read manual explaining how to use WOR but I am not sure how to use that. 

1. Is it fine to use Universe(gro, trajectory) where the trajectory is in the format of gro?

At the moment, we do not support trajectories in GRO format, only a single frame. Can you convert it to XTC or TRR?

2. In the select line, I am totally lost. I want to reproduce the data generated by the reference in the manual regarding the WOR. But I am confused of which word should I use.

Can you show us the code that you are writing and all output that you get? Then we can help with specifics.

If you haven’t dones so already, have a look at the Quickstart Guide https://userguide.mdanalysis.org/stable/examples/quickstart.html and the documentation in the User Guide to learn more about selections https://userguide.mdanalysis.org/stable/selections.html.

Oliver

Can anyone help me to figure it out?

Thanks in advance and with my best regards

--

Oliver Beckstein (he/his/him)

orbe...@gmail.com