[gmx-users] Single point energy calculations

[soumadwip ghosh]

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?

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

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?

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?

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

Thanks and regards,
Soumadwip Ghosh
Senior Research Fellow
IITB
India