Re: NAMD/VMD installation for Windows 10

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon Nov 19 2018 - 10:59:48 CST

Hello,

I haven't used the Windows subsystem for Linux - WSL (I prefer cygwin
for my bash addiction when using windows, and, of course, native linux
itself).

 From a quick search, I saw that it pretty much uses a similar
philosophy as cygwin, at least as far as the paths are concerned.

1.  Your actual C: drive (and everything you have on Windows) can be
accessed from the subsystem as "/mnt/c".  Therefore, if you have namd in
a directory like "C:\NAMD2", you could invoke it as "/mnt/c/namd2".

2. Your home directory is Linux-like, i.e. "/home/yourusername". This is
located in the WSL's installation paths (which I believe are somewhere
in "C:\Users\yourusername\AppData".  Most importantly, this home
directory contains ".bashrc" and other similar files, which you can edit
to add extra features to your bash console, such as command aliases or
append paths to the bash $PATH variable.

For example, you can use an alias for namd2 like the following:

alias namd2="/mnt/c/NAMD2/namd2"

or append it to the PATH like this:

export PATH=$PATH:/mnt/c/NAMD2

This way, you could simply call namd2 like any other command, without
having to use its path.

Overall, it seems your problem is understanding how the WSL (and
probably Linux and Unix in general) works, rather than namd and VMD
themselves.  Therefore, I doubt that anything more technical on VMD and
NAMD offered can help you until you fully familiarize yourself with the
system.

You should read Microsoft's manual for the WSL and fool around:

https://docs.microsoft.com/en-us/windows/wsl/interop

Good luck,

Fotis

On 11/19/18 6:27 PM, Joey Gehring wrote:
> Hello!
>
> I am a former physics student that recently graduated that used NAMD
> and VMD on a windows 7 machine in college. I am now an owner of a
> windows 10 machine utilizing windows subsystem for linux. I absolutely
> love the bash command line. I am eager to successfully install NAMD
> and VMD, however I am running into issues. I am easily able to install
> VMD with no problems at all, however, I cannot seem to successfully
> run it from a simple namd2 or vmd command. I think that this has
> something to do with setting the environment variables correctly.
>
> In short, I would very much appreciate a beginners guide for getting
> NAMD/VMD up and running and successfully installed on my machine.
>
> From what I know, I simply need to untar or unzip the compressed NAMD
> folder into my C:// drive and then use the vmd wizard to successfully
> install vmd. I thought this was it. What am I missing?
>
> Cheers,
>
> Joey
>

-- 
*******************************************
Fotis A. Baltoumas
Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology, National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************

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