[gmx-users] LJ Plot

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> 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.
> 

Then it sounds like you've found your solution:

http://lists.gromacs.org/pipermail/gmx-users/2010-December/056437.html

Otherwise, it is trivial to write a simple program to plot these two functions 
using the standard form of the Lennard-Jones equation.

-Justin

>> 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
>>>>>>
>>>>>> ========================================
>>>>>> -- 
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> 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
>>>>
>>>> ========================================
>>>> -- 
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>
>>
>> -- 
>> Massimo Sandal, Ph.D.
>> http://devicerandom.org
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 

-- 
========================================

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

========================================