On 20/09/2012 4:21 PM, tarak karmakar wrote:
Thanks Mark.
I was using the following command as I got it in the manual.
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg
But I could not able to find the way how to specify the indices of the
two desired atoms.
( suppose I want to plot the distance between atom no. 500 (protein
backbone) and atom no. 879 (ligand atom) with respect to time)
See manual 8.1 for discussion, and
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx for more.
Mark
On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham <[email protected]> wrote:
On 20/09/2012 2:05 PM, tarak karmakar wrote:
Thanks Justin.
But in my case I want to plot the distance between one atom in the
backbone of the protein and other atom present in the ligand. Then how
can I specify these two atoms I need for plotting the distance between
them.
g_dist treats the system as a list of atoms, and is ignorant of details like
molecules. So you just need to tell it which atoms via their indices.
Mark
On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul <[email protected]> wrote:
On 9/19/12 2:55 PM, tarak karmakar wrote:
Dear All,
I want to calculate the distance between the nitrogen atom present in
the ligand and the H- attached to the backbone of the protein along a
long trajectory. So can anyone suggest me how to consider these two
atoms to calculate and plot the distance along with the time ?
g_dist with appropriate index groups.
-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
========================================
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