[gmx-users] residue-residue interaction energies

federico vaglio federico.vaglio at gmail.com
Mon Oct 8 09:14:44 CEST 2012

Hi Justin,
thank you for your quick reply.

When you say:

"..Probably by analyzing them individually with mdrun -rerun to recalculate
each frame.  Tedious, but can be easily scripted..."

do you mean I have to run g_enemat module using -b and -e options in order
to set the first and the last frame to read from trajectory?
If not, could you please suggest me the correct way to do so?

thank you again.


On Sat, Oct 6, 2012 at 4:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 10/5/12 1:40 PM, federico vaglio wrote:
>> Dear all,
>> I would like to extract the interaction energies (LJ
>> and electrostatic) between each residue pairs from my trajectory.
>> The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm,
>> LJ-SRemat.xpm, totalemat.xpm) but not a "data" file with
>> the residue-residue interaction energies I'm looking for.
>> Is there a way to get these numbers? Or have I to read the xpm "matrix"
>> and
>> convert all those letters to the corresponding energy values?
> Yes, you have to map it out based on the .xpm labels.
>  Finally, is there a way to get pairwise residue-residue interaction energy
>> values from each snapshot of my trajectory ?
> Probably by analyzing them individually with mdrun -rerun to recalculate
> each frame.  Tedious, but can be easily scripted.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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