Re: how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 20 2019 - 14:42:13 CDT

Hi Jiali, the tutorials are examples, and can never list all supported
options. What you are looking for is a *manual*.

Pmepot has its own webpage, while the "volmap" command (independent from
the GUI) is documented in the VMD manual.

Giacomo

On Wed, Mar 20, 2019 at 10:56 AM jiali wang <jialiwangnamd_at_gmail.com> wrote:

> Hello Dear Giacomo,
> Thank you so much for your quick response. Actually I go through
> all the tutorials, for PMEplot,it mention use "pmepot -all" to calculate
> all frames, but it only provide a average,not to create a every frame PME
> trajectory.
> Also i am more interesting in concentration plotting, in "volmap density"
> command, I didn't find any option to help me calculate every frame
> individually, and mix them together to make a movie. also i tried to load
> every dx file together, it's not working. If you could provide me some
> example?
>
> Very appreciate your help and thank your for your time.
> Jiali
>
> On Wed, Mar 20, 2019 at 9:11 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Jiali, pmepot (and the volmap command, which computes density maps)
>> have flags to select single frames or a range of frames, thus generating
>> multiple maps instead of a single one containing the average of the whole
>> trajectory.
>>
>> You can then load each DX map in memory on its own, preferably with a
>> script if you have many.
>>
>> Giacomo
>>
>> On Tue, Mar 19, 2019 at 9:02 PM jiali wang <jialiwangnamd_at_gmail.com>
>> wrote:
>>
>>> Hello everyone,
>>> by study the tutorial in "Electrostatic Maps and Ion Conduction" ,I
>>> understand using
>>> *pmepot -sel $all -frames all -xscfile cntwieq-01.restart.xsc -grid {48
>>> 48 48} -dxfile eqpot.dx -ewaldfactor 0.25 *could generate a dx file to
>>> showing the elestractic potential, and also can create a water density
>>> maps.
>>> but this more like a average of all frame calculation, can some one tell
>>> me how to generate a Dx. movie? to calculate every frame and make it a
>>> movie. not average of frames.
>>> Very appreciate your help.
>>>
>>> best,
>>> Jiali
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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