[gmx-users] Energy drift

Xiaobin Cao xcao at lsu.edu
Wed Aug 20 06:48:56 CEST 2014

Thank you, Mark. I am following this paper: "Mutual diffusion coefficients of heptane isomers in nitrogen: A molecular dynamics study" (JCP, 2011). They use flexible model, so do I (please check my top and mdp files). Actually I already checked the time step of 0.5fs, and it does not work. Belows are their description for their system:

They use the potential parameters I attached for N2,  but I am not sure if they assign charges on N atoms. Lennard-Jones 12-6 potential is used to describe interactions between molecules. 
NVT ensemble and PBC are used, and the cutoff is 18 A.
 The initial velocities of the molecules were derived from the Boltzmann distribution. 
The Verlet leapfrog numerical integration algorithm was employed with a time step of 1.0 fs. 
The total simulation time was 14 ns and the sampling time for the velocity correlation was chosen to be 7 ns for the temperature range considered. 
The velocities and positions of the molecules were recorded every 50 time steps.  

Thank you

Date: Tue, 19 Aug 2014 14:35:51 -0500
From: Mark Abraham <mark.j.abraham at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Energy drift
        <CAMNuMAQ5jiQeaFFBRk2sdp5s0mjtMpU5dfq=FPAno221co=Q2w at mail.gmail.com>
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Hopefully you are following some established protocol for your N2 model. If
so, use its recommendation for time step and or bond constraints. Not using
constraints can lead to your symptoms with 1fs time step - prefer 0.5fs.


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