VMD-L Mailing List

From: andrea spitaleri (andrea.spitaleri_at_iit.it)
Date: Thu Jan 22 2015 - 04:40:35 CST

In addition to it,

I post-process my ppm file to convert to jph by convert command adding
the time frames too. In the dir with the ppm files:

###
i=1
find . -name "*.ppm" | while read line
do ts=$(echo $line | awk -F . '{print $3}')
rt=$(expr $ts \* 10)
new=`echo $rt | awk '{print $1/1000," ns"}'`
echo $i
i=$((i+1))
convert -resize 668x832! -font helvetica -fill red -pointsize 36 -draw
"text 70,95 '$new'" $line foons.$ts.jpg
done
###

the frame number is taken from the number of the file and then converted
it to time (first in ps and then in ns)

afterwards just merge the jpg files to mp4 as previously said.

Hope it helps

and

On 21/01/2015 16:18, Norman Geist wrote:
>
> At each frame the time can be computed as:
>
> t[µs] = frame * timestep * dcdfreq * stride / 10-6
>
> To print it to the screen, the “draw” command can be used.
>
> But to update it everytime the frame changes, you’d need to write a
> tcl procedure and register a trace on the moviemaker frame. This proc
> must also delete the print of the previous frame. If you use “Userani”
> from the VMD script library this would be quite easy to do. Otherwise
> you need to follow the examples for the “user defined procedure” in
> the VMD movie maker.
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/usermovie.tcl
>
> Let me know if you need further assistance.
>
> Norman Geist.
>
> *Von:*sunyeping [mailto:sunyeping_at_aliyun.com]
> *Gesendet:* Mittwoch, 21. Januar 2015 15:30
> *An:* Daniel Möller; norman.geist
> *Cc:* vmd-l
> *Betreff:* Re: AW: vmd-l: The quality of movie made by VMD
>
> Dear Daniel,
>
> Thank you a lot. You reply is very helpful. But could you tell me how
> to show the simulation time (us) in the VMD window?
>
> Best regards.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
> ------------------------------------------------------------------
>
> From:Daniel Möller <daniel.moeller3_at_uni-greifswald.de>
>
> Send Time:2015年1月19日(星 期一) 23:35
>
> To:孙业平<sunyeping_at_aliyun.com>
>
> Cc:vmd-l <vmd-l_at_ks.uiuc.edu>
>
> Subject:AW: vmd-l: The quality of movie made by VMD
>
> Hi,
>
> as additional information my configuration for ffmpeg:
>
> ffmpeg -an -i /tmp/movie.%05d.ppm -vcodec mpeg2video -q 1 - s
> hd1080 /tmp/movie.mpeg
>
> -an (audio disabled); -i (input files; you can’t change the number
> part, so don’t have more than 10000 frames (0-99999)); -q (quality
> - 1 (best)); -s (size; look in the help or the internet which you
> need/want)
>
> more: -r (fps); -vstats_file /tmp/log.log (output in a file)
>
> I hope this helps.
>
> Daniel Möller
>
> *Von:*owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Norman Geist
> *Gesendet:* Montag, 19. Januar 2015 09:41
> *An:* 'sunyeping'
> *Cc:* VMD Mailing List
> *Betreff:* AW: vmd-l: The quality of movie made by VMD
>
> Hey,
>
> this is related to the default options VMD passes to the program
> which actually links all the pictures made by VMD to a video file
> at last. You can disable the option to “delete image files” under
> “movie settings” in the movie maker window and use ffmpeg or
> ppmtompeg later manually, using higher quality settings. You will
> usually find all the pictures in /tmp.
>
> You might also be interested in
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/userani/for
> easy animations in movies.
>
> Also the best renderer is actually Tachyon. Optionally by enabling
> “ambient occlusion” and “shadows” under VMD
> Main->Display->DisplaySettings, but this makes it way slower.
>
> Norman Geist.
>
> *Von:*owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>
> [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im Auftrag von *sunyeping
> *Gesendet:* Montag, 19. Januar 2015 04:46
> *An:* vmd-l
> *Betreff:* vmd-l: The quality of movie made by VMD
>
> Dear VMD users,
>
> I am preparing movie from my MD simulation trajectory using the
> movie maker plugin of VMD. But I find the quality of the movie I
> made is unsatisfying when comparing with those published. For
> example, the movie published by DE Shaw
> (https://www.dropbox.com/s/e9grvp8f9mnkopx/movie_Shaw.mov?dl=0)
> has a higher solution than mine
> (https://www.dropbox.com/s/2qi0tgm6oag4lox/movie_Sun.mp4?dl=0). I
> have the following question:
>
> (1) I made my movie as mpg format with VMD and then save it as mp4
> format with VideoMach. Was Shaw's movie also made by VMD and and
> VideoMach? Or was it made by other software?
>
> (2) What is the representation of the structure in Shaw's movie? I
> guess it is Cartoon/New Cartoon in VMD. But when applying
> Cartoon/New Cartoon representation in my structure, it doesn't
> look as beautiful as Shaw's.
>
> (3) I use POV-Ray render in VMD which generate images with the
> higher solution than any other reder setting. But the solution is
> still lower compared with Shaw's movie. How was Shaw's movie rendered?
>
> Thanks in advance.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
> 

-- 
Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557