On 10/8/12 3:14 AM, federico vaglio wrote:
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?
Not what I was suggesting, but using -b and -e should also work.
-Justin
thank you again.
Federico
On Sat, Oct 6, 2012 at 4:54 AM, Justin Lemkul <[email protected]> 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
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========================================
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
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