Hello,
I have simulated a metalloenzyme, containing zinc, in gromacs for
100 ns. When i plot distance between zinc and a specific atom in protein,
the plots obtained are different in vmd and gromacs (using gmx distance).
vmd shows that the zinc has moved out of the protein at the end of
Thank you very much Eric Smoll!
I will use "tc_grps = Protein Non-Protein".
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Jan 28, 2019 09:45 AM
To: "gromacs.org_gmx-users";
Subject: What is the difference of using "system" and
Hello Neena,
These links should help.
http://www.gromacs.org/Support/Mailing_Lists
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
The first link seems to suggest that a standard search with a search engine
like Google should scan the Gromacs archive entries.
The second link
Hi Gromacs users,
Is there a quick way to scroll through previous questions in the mailing list?
Now, I am able to control find my question of interest only for each month
separately. Can I look through the entire log file from 2000 till now at once?
Thanks,
Neena Eappen
Graduate Student
Hello,
The following link should help.
http://www.gromacs.org/Documentation/Terminology/Thermostats
Best,
Eric
On Sun, Jan 27, 2019 at 6:46 PM ZHANG Cheng <272699...@qq.com> wrote:
> In the mdp file, I am using "tcoupl = v-rescale".
>
>
> Is there a difference between using "system" and
Hi Mark,
I looked the combined trajectory with VMD by loading the gro and xtc files,
and the ensemble looks messy (the ligand is flying away from the protein).
I am not sure which step could be causing the issue. But I want to describe
what I have done to the trajectory file from the beginning
