[gmx-users] LJ Plot

[nishap.patel at utoronto.ca]

Quoting ms <devicerandom at gmail.com>:

I did two different simulation. One with van der Waals attractive term  
and one without van der Waals attractive term. And so to see the  
difference between the LJ potential between the two simulation I  
wanted to plot the LJ potential for both the simulations and  
superimpose them. Because if there is no attraction LJ-12 (i.e. 1/r^-6  
set to zero )LJ potential plot would be different than the one with LJ  
6-12 potential.

> On 06/12/10 23:26, 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.
>
> 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.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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>>
>>
>>
>>
>
>
> -- 
> Massimo Sandal, Ph.D.
> http://devicerandom.org
> -- 
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