[gmx-users] LJ Plot

[Mark Abraham]

On 12/07/10, nishap.patel at utoronto.ca wrote:
> Quoting "Justin A. Lemkul" <jalemkul at 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.
> 

g_sigeps -c6 0 probably does that. See g_sigeps -h

Mark

> 
> >
> >
> >nishap.patel at utoronto.ca wrote:
> >>Quoting "Justin A. Lemkul" <jalemkul at 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.patel at 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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> 
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