[gmx-users] Single point energy calculations

Mark Abraham mark.j.abraham at gmail.com
Tue Aug 25 09:39:10 CEST 2015


On Tue, Aug 25, 2015 at 6:30 AM soumadwip ghosh <soumadwipghosh at gmail.com>

> Hello all,
>             I am trying to calculate the single point energies of my system
> (a nucleic acid and a nanoparticle) to ultimately estimate the
> E(interaction). I am following this paper.
> http://ac.els-cdn.com/S0045653513001215/1-s2.0-S0045653513001215-main.pdf?_tid=cc0e4256-4add-11e5-8426-00000aab0f26&acdnat=1440475397_d1db3b13c45b5048a7722828548fb29e
> It was written that
> Eint= Etot- (EC60+ELOA)
> Where ETOT is the potential energy of the  LOA-C60 system and E60 and ELOA
> are the single point energies obtained by stripping the LOA or the C60 from
> the equilibrium geometries of the LOA-C60 system. I have no idea how to
> calculate this single point energy. I have checked some of the discussion
> threads in GROMACS archive and also the single point webpage of GROMACS
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Ene
> <http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy>
> Regarding this I have some questions.
> 1. Is the .tpr file fed to grompp with -rerun generated by using a  .top
> file consist only of the structure in the configuration.pdb file?

The .tpr must match the configuration, as it says at that link.

> 2. What parameters one should use in the corresponding .mdp file?

Whatever describes the model you want mdrun to implement, just as with
normal simulations (e.g. cutoff, electrostatics model) but things related
to update schemes (e.g. time step, thermostat) don't apply.

> 3. In some of the discussions I saw people used minim.mdp as well as md.mdp
> files with nsteps= 0. Which one to consider?

Neither, per above link.

> 4. After the mdrun I am supposed to get am .edr file. Is the single point
> energy correspond to the potential energy in it or is it explicitly written
> elsewhere ( .log file) or is it some other energy term?

The .edr will have the potential energy, and various of its components. The
.log file probably also has a version of it at lower precision.

I would appreciate any sort of help. I have never done single point energy
> calculations using MD simulations and sorry for asking much.

You have all the information you need - go do it! :-)


> Thanks and regards,
> Soumadwip Ghosh
> Senior Research Fellow
> India
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