Thank you for your suggestion.
- Message from David van der Spoel -
Date: Thu, 2 Jan 2020 08:28:17 +0100
From: David van der Spoel
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] lifetime of hydrogen bond
To: gmx-us...@gromacs.org
Den 2020-01-02 kl. 07:47
Den 2020-01-02 kl. 07:47, skrev sp...@iacs.res.in:
Dear all
I want to calculate the hydrogen bond lifetime of a dynamic hydrogen
bond which stays for say 10 ns (as I have saved the trajectory with 10
ps interval). I am trying to calculate the lifetime of this hydrogen
bond by gmx hbond
Dear all
I want to calculate the hydrogen bond lifetime of a dynamic hydrogen
bond which stays for say 10 ns (as I have saved the trajectory with 10
ps interval). I am trying to calculate the lifetime of this hydrogen
bond by gmx hbond command
gmx hbond -f traj_nopbc.trr -s md.tpr -n
I mean't to type that the expected value should be around 0.27ps but I am
getting 2 to 3 ps from my simulations. The autocorrelation function decays to
0. Is there something I am missing? Any insight would be appreciated. Thanks.
Emvia
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Hello all, I am finding the lifetime of hydrogen bonds between water molecules
for various systems. To compare my values to bulk I have determined bond
lifetimes of a 4x4x4 nm3 box of spc/e water. The expected lifetime should be
around 0.27 seconds, however i am obtaining values around 2.1 to
