[gmx-users] Energy of part of system

[Beniamino Sciacca]

Thanks very much!
So using g_energy I choose
LJ-SR:DNA1-DNA2
LJ-SR:DNA2-DNA3
LJ-SR:DNA1-DNA3
Adding these three terms I obtain the total interaction energy between 
the DNA molecules, isn't it?
There is a lot of difference between LJ-SR..... and Coulomb-SR.
Which is the best method to estimate this interaction energy (LJ or 
Coulomb)?
Beniamino

leafyoung81-group at yahoo.com ha scritto:
> Then you shall make them as a group before the simulation...
>
> Fortunately, there is -rerun for mdrun.
> I suggest the following way:
> 1. Use make_ndx to make groups for three DNA molecules respectively, 
> namely d1, d2 and d3. The 4th groups is of course sol.
> 2. Set unconstained_start=no in the mdp file.
> 3. Set energygrps=d1 d2 d3 sol in the mpd file.
> 4. Use mdrun -rerun your.xtc
>
> Yang Ye
>
> ----- Original Message ----
> From: Beniamino Sciacca <superbenji83 at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wednesday, June 21, 2006 10:26:05 PM
> Subject: [gmx-users] Energy of part of system
>
> Dear gmx user,
> my system is: three DNA molecules solvated in water and ions.
> At the end of md I would to know the interaction energy between the
> three molecules of DNA.
> How can I do?
> If I use g_energy and I choose "Potential" I obtain the potential energy
> of the whole system, isn't it?
> But I want the interaction energy.....
>
> Thanks in advance
> Beniamino Sciacca
>
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