[gmx-users] Single point energy calculations

[Mark Abraham]

Hi,

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

> 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! :-)

Mark


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