[gmx-users] LJ Plot

[nishap.patel at utoronto.ca]

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.
>
>
> 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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