Then what is the right way to calculate lifetime of a hydrogen bond?
- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -
Date: Mon, 13 May 2019 22:24:51 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re:
In gromacs you can not calculate h-bond life time. You can use mdanalysis
tool for calculating h-bond lifetime.
On Tue 14 May, 2019, 11:56 AM , wrote:
> Then what is the right way to calculate lifetime of a hydrogen bond?
> - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
>
Dear GROMACS members,
I would like to calculate the Young's modulus for crystalline cellulose.
I simulate the system using NPT ensemble with anisotropic barostat.
I apply a constant stress in a given direction. For instance, I apply a
constant stress in XX direction and set the compressability
Hi
In md analysis you can calculate continuous h-bond. That will give you
proper lifetime.
On Tue 14 May, 2019, 11:58 AM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in>
wrote:
> In gromacs you can not calculate h-bond life time. You can use mdanalysis
> tool for calculating h-bond lifetime.
On 5/14/19 10:34 AM, CROUZY Serge 119222 wrote:
Hello Jon and Justin
I had a MD simulation "dyn" running for 46 ns (actually it's 30 umbrella
simulations using pull code)
I did try the -cpi option and my calculation seems to have restarted correctly
renaming the files dyn.part0003
But
Hello Jon and Justin
I had a MD simulation "dyn" running for 46 ns (actually it's 30 umbrella
simulations using pull code)
I did try the -cpi option and my calculation seems to have restarted correctly
renaming the files dyn.part0003
But just running
gmx mdrun -cpi -noappend
does not
