[gmx-users] Some simple questions about using -rerun in mdrun for energy between two groups

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 18 18:37:51 CEST 2016


This just works on the original trajectory if you use energy groups in the
rerun tpr. Whether the numbers are useful is another matter :-)


On Mon, 18 Apr 2016 18:27 Sheng Bi <chrishengbee at hust.edu.cn> wrote:

> Dear GMX Users
> I have some questions when using -rerun in mdrun to get some specific
> energy for my groups. Let me describe my question in this way.
> I have a system containing some groups which include A and B and others.
> My goal is to calculate the energy between A and B.
> So Here is my steps:
> first, I use gmx trjconv to get trajectory contains only A and B called
> A_B.xtc.
> Second, I grompp a new tpr which is also only contain group A and B called
> A_B.tpr.
> Third, I use mdrun -rerun A_B.xtc -s A_B.tpr -v -deffnm energy_A_B
> Last, I use gmx energy -f energy_A_B.edr and choose "Total Energy" to get
> total energy of A_B system.
> My question is, by this way, I can get the total energy (name it E_total),
> but in my opinion this energy is composed of the energy
> between A and A (name it E_A_A), energy between B and B (name it E_B_B),
> and energy between A and B (name it E_A_B). I only care
> about E_A_B. By now, I have to repeat above four steps to get E_A_A, and
> E_B_B, then use E_total minus E_A_A and E_B_B to get E_A_B.
> This is a very tedious work.
> I am not quite familiar with -rerun, Is there any ingenious method to get
> E_A_B ? I am not quite familiar with -rerun?
> Thanks
> Sheng bi
> --
> PhD student
> State Key Laboratory of Coal Combustion,
> School of Energy and Power Engineering,
> Huazhong University of Science and Technology (HUST),
> Room 302 Power Building,
> 1037 Luoyu Road, Wuhan, Hubei 430074 China
> Email: chrishengbee at hust.edu.cn
> Phone: (86)27-87548122
> http://itp.energy.hust.edu.cn
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