Dear gmx-users,
Q1) I would like to plot the radius profile of a water droplet on graphene, as a function of z-direction, as per below:
http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/large
Which GROAMCS utility should I use, and how do I go about plotting the profile?
Q2) Another question that I have is, suppose I have equilibrated (NVT) a water droplet for 10ns, and would like to plot the H-bond density (along the z-direction),
I type the following command:
g_density_mpi -f traj_comp.xtc -n system.ndx -s topol.tpr -b 9000 -e 10000 -sl 1000 -dens number -o number-density-OH.xvg
I was only able to select:
System
Graphene (my substrate)
Water
How can I create a system.ndx such that it allows me to choose the OH (instead of water)?
Q3) Regarding Q2, the g_density_mpi utility read the frames contained within the time frame of 9 - 10 ns, but does it average the frames to give a time-averaged density.xvg?
Thank you for your time, any feedback is appreciated.
Merry Christmas & Happy New Year!
Regards,
Kester
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