On 1/21/13 8:27 AM, biki wrote:
Hi ,
I am doing a simulation of 32 spce water molecules using Gromacs-4.5.5 version.
I need to calculate the force on each hydrogen atom of each water molecule due
to all other atoms on rest 31 water molecules. I have generated the force.xvg
file and I know that it will print the x,y and z component of force on each
hydrogen as a function of time. But when I opened it in vi editor, it was not
legible at all. I have attached a snapshot of force.xvg file here.
Can any one please explain how this force.xvg file is arranged?
Is there any way to write these forces in a format mentioned below by using
gromacs utility
time step
x-component of force on Hydrogen1 y-component of force on Hydrogen1
z-component of force on Hydrogen1
x-component of force on Hydrogen2 y-component of force on Hydrogen2
z-component of force on Hydrogen2
.
.
.
so on....
That's what you have, but since it's a time-dependent quantity, these values are
printed for every frame in the trajectory. Note the legends present. You have
96 atoms, each with the (x,y,z) components of the force printed for each frame.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
