0:14 all right until now we have installed
0:18 chromax how however chromax is only a
0:20 simulation Engine with some analysis
0:23 tools to study molecular systems we also
0:27 need a visualization program to check
0:30 and run the structures some of the best
0:32 visualization software that works well
0:39 with gromax u chier x pyo and vmd in
0:42 this Workshop I'm going to use vmd
0:47 because it's mostly written in C and
0:52 C++ so it's very fast and efficient and
0:54 is capable of handling very large
0:56 molecular systems and it offers a good
1:00 collection of analytical tools also in
1:04 vmd you can automate tasks using TLC
1:07 scripting and because vmd has a large
1:11 community and extensive documents so in
1:13 this video I'm going to teach you how to
1:16 install vmd on a Linux machine first
1:17 thing first you need to download the
1:20 code from the vmd
1:24 website uh from here download
1:26 vmd and here I'm going to choose the
1:30 latest version of vmd which is vmd2
1:40 Linux all right vmd is a free software
1:43 but you have to create an account in the
1:56 one I agree
2:00 and okay here I'm going to choose vmd2
2:16 Linux and now I have vmd in my download
2:18 folder all right first we need to
2:20 extract the file and I'm going to
2:27 desktop using the to command and the
2:34 here till the sign means home folder
2:37 because downloads is in the home folder
2:40 and we also need
2:44 xzf options because this is a tajz file
2:47 and finally the name of the file which is
2:49 is
2:56 Taj all right it has created a fold on
3:01 my desktop which contains vmd files
3:04 and first I'm going to enter the folder
3:07 using CD command let's see what's inside
3:09 the folder all right this is a binary
3:12 package and all we need to do is edit
3:15 this file the configure
3:20 file I'm going to open it using VI by
3:22 the way you can edit the file using any
3:24 text editor okay here I'm going to
3:27 specify the location of the installation
3:31 and I want to install it in the op
3:35 folder alongside chromax so I'm going to
3:41 change this line op and vmd
3:45 2.0 and
3:48 Bin and we need to specify the location
3:56 files let's put it in opt
4:10 lib now I'm going to save the file and
4:13 execute the configure
4:18 file and finally so do make
4:27 enter all right I've made a mistake
4:38 folder and then execute the make install
4:41 command okay let's check the
4:44 installation op and
4:48 vmd and the final step is to introduce
4:51 the vmd folder to The Bash shell and if
4:54 you don't know bash is this text based
4:57 environment and the reason is that when
5:00 we summon the vmd command the B shell
5:03 don't know where is the vmd binary file
5:06 and its Library files and actually this
5:08 is a really easy job all we need to do
5:12 is open
5:16 the do bashrc
5:19 file and at the end of the file we need to
5:22 to
5:25 add this
5:28 line path
5:30 equals the path
5:36 and opt and vmd
5:38 vmd
5:42 2.0 all right and then I'm going to save the
5:43 the
5:46 file finally I'm going to restart the B shell
5:48 shell
5:51 exit and open it
5:55 again now I can execute the vmd command
5:58 in any location in any directory by
6:12 system the final note is that you don't
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