VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sat Jan 14 2017 - 11:59:46 CST

>
> *As i load the gro file and the in second step i load the trr.file..now
> can both are loaded simultaneously ,,i mean on Open GL window only one
> molecule will be loaded at a time.*

I am not sure if that is a question or a statement. But I will comment on
it none the less.

With VMD -- what happens is that you first load a structure file and then
in the next step load information on top of it. Both of these two files
(structure and trajectory come in different forms). You need to have both
before you can do any form of analysis. The OpenGL window that you refer to
is called the Display window. This window will show you your system once
its properly loaded. Another window which is also open at this same time is
VMD Main window. In this window there is a black slider at the base of the
VMD Main window. If you have loaded a trajectory file having more than 0
frames you should be able to scroll this slider from left to right. As you
do this the VMD Display window will show the protein / system move. This
movement (which is what your simulation generated) is basically what your
analysis will be based on.

*segmentation fault*

A number of factors could be causing this. Size of your trajectory vs how
much memory you have in your computer. Instead of loading the complete trr
file you can load a small part of it. To load a small part of it, when you
load the trr file (browse molecule window) there is a 3 box pane two of
which say first and last. In the first keep value at 0 and in last put a
small number say 5 or 10. This would then load only 6 or 11 frames and you
can use the slider to move around. Could you tell us the size of your
protein - ligand system (i.e. how many atoms are basically in your system)?
How many frames are in your trajectory? Is your computer running windows or
linux and is it 32 or 64 bit? Which version of VMD are you using?

*one more thing i would add should i learn language for the using Scripts
> of VMD.*

To stay inside VMD you need the language called "TCL". The short scripts
that I sent earlier were written in TCL format. If you want to not use VMD,
it can both be little easy or complicated. E.g. just some simple bash
(linux shell) commands originating from GROMACS can generate your plots for
you - which is the easy way If you are wanting some additional analysis
(like the awesome stuff) you would need something that provides a bit more
here VMD fits in nicely, otherise you can go for external python (or other
language) packages for analysing your data.

*how can i learn all the basics about computing*

In my experience there is no such thing is knowing everything especially in
the area of research. I believe that there are two ways of knowing "a lot"
not all.

1) you want to be a developer - in which case you need to know about stuff
that is already out there. You need very good coding practice. You need to
write clean code which is optimised for running across various platforms
etc. This is something that a developer does, in which case knowing a lot
is absolutely necessary.

2) you are a researcher - and just want to write short scripts to get your
job done. This is what you are doing now. Going about the web, reading
manuals, messaging mailing lists etc. In this category you collect just
enough information to get your job done.

Note that in both of the above categories no one knows everything. There is
always room to learn more/new stuff.

*that can help me in my computational biochemistry and using different
> softwares*

Using software doesn't require knowing how to code. Most of the tools that
I have come across are usually made simple enough that the end user can run
it with a few clicks/commands. If you want to know about how to do well in
the area of computational biochem I would recommend the following::

1) Use Linux. Although windows looks friendly and linux may appear
challenging at first you will do very well in the long run.
2) When you start using Linux learn to write short bash scripts or one
liners to get some of your work done.
3) Know how to handle at least one language properly (again I recommend
python but other include perl or you could do an environment like R) but
choose something that has a large user community so if you run into
problems you can find solutions.
4) Know some form of plotting tool well. xmgrace, plotting functions in R,
or use libraries like matplotlib.
5) These are just the things I know. These are by no means exhaustive - but
they get my job done for me. Depending on what area you specialise in you
will be doing something similar to this so perhaps start with this list.

*as u talked about plugins so now this a very confusing term for me that
> what is the purpose of plugins and how it can be installed and how to get
> its working by installation.*

I am not sure about the exact definition of a plugin myself. They are
basically short targeted programs that carry out specialised tasks. They
are integrated into the bigger environment of VMD. To put simply (i
think!!) when you pressed Analysis > RMSD trajectory -- you were accessing
a plugin. I believe most of the plugins are already inside VMD. Under
analysis and you don't need to install them. Everything you find in the
graphical user interface can be coded. E.g. the script (bunch of lines)
that I wrote earlier for RMSD calculation is basically what the RMSD
trajectory tool will do as well (but it will generate the plot for your as
well if you have enabled that when you compute RMSD).

*As MD simulation i think demands for all these basics. *

If you plan on doing MD simulations, choose one environment and at least
for now stay with one. If you plan on depending on VMD, then perhaps it
would be better that you used NAMD with CHARMM forcefields for your
simulations and then do all the analysis you want with VMD. For a startup
user, everything is present inside the VMD GUI.

Hope this helps.

On Sun, Jan 15, 2017 at 2:50 AM, maria khan <mariabiochemist1_at_gmail.com>
wrote:

> one more thing i would add should i learn language for the using Scripts
> of VMD.
>
> and i will ask u another important point that is,,im a non computer master
> how can i learn all the basics about computing that can help me in my
> computational biochemistry and using different softwares..as u talked about
> plugins so now this a very confusing term for me that what is the purpose
> of plugins and how it can be installed and how to get its working by
> installation.As MD simulation i think demands for all these basics.
> Thanks for help.
> 

-- 
Best,
/A