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
[EMAIL PROTECTED] 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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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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