[gmx-users] LJ Plot

[ms]

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