On 06/12/10 23:26, nishap.pa...@utoronto.ca wrote:
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
I actually want to plot my simulation with ad without the attractive
term C6 of van der Waals and superimpose them to see the difference.
The expression "plot my simulation" makes no sense. You don't plot a
simulation, you plot variables calculated from a trajectory.
Also, what does it mean "with and without the attractive term"? You
perhaps want to *do* two different simulations?
nishap.pa...@utoronto.ca wrote:
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
How does sigeps read the input file? I tried using sigeps to plot LJ
for different solutes in solvent and it gives me the same C6 and C12
value, when it runs, which seems a weird.
c6 = 1.00000e-03, c12 = 1.00000e-06
sigma = 0.00000, epsilon = 0.00000
Van der Waals minimum at 0, V = nan
g_sigeps does not take any input file. It produces an LJ curve based
on command line parameters. I guess this is not what you are after,
although that's exactly what it sounded like from your last post.
Perhaps you need to re-phrase your question. If you just want to plot
van der Waals energy terms, use g_energy to pull them out of the .edr
file.
-Justin
Is it the default?
nishap.pa...@utoronto.ca wrote:
Hello,
Is there an option to plot Lennard Jones potential? I tried looking
through the list and manual but I did not find any suggestions on
how I could plot a LJ 6-12 potential plot.
g_sigeps
-Justin
Nisha
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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