Hello,
I have run a simulation of amino-acid +water system in GROMACS software. Now i need to get the water orientation profile (ie., how the water molecules are oriented w.r.t specific atom/moiety say, water orientation towards C-alpha, etc.,)
I tried with the commands like gmx sorient, gmx h2order, but in vain...and i am expecting graphs like from the literature survey (the screenshot images are attached).
So, is it possible to get the water orientation profile/cos theta distribution functions using in house gromacs commands or any other ways ..??
Any suggestions are appreciated.
Thank you.
Hi there,
you should have a look to the molecular dynamics analyzer Travis. http://www.travis-analyzer.de
Such features must have already been implemented in the code.
Cheers
Romain.
Dear Dilip,
Travis is a choice.
You could also use a tool developed in my previous group, you can find it here:
https://gcm.upc.edu/en/members/luis-carlos/angula/ANGULA.
You could take a look at a paper using it:
Article On the positional and orientational order of water and metha...
Hi, I usually do this in Gromcas for the orientation of water in ions, you have to have a good index file or otherwise It will do nothing good.
What is the water model that you use?
Because for me the SPC/E work fine, but for the SWM4-NDP I have issues, so I use a personal code but I have to use g96 configuration format files
- Badges
- Science topic