VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Feb 08 2007 - 17:13:52 CST

Hello Matt,

First of all, I think that would be nicer from you if you try to calm
down and look for better alternatives to solve the problem. You have
to remember that the developers and the rest of us who contribute a
little bit to keep up this list do it without getting any extra penny.
Moreover, if you compare the help you get from software vendors (many
of these programs are very expensive) and from the VMD people, you'll
find a huge gap between what you pay and what you get (VMD costs you
$0.00 and gives you a lot). So I think you have to be more careful
with what you say. If you're not happy with VMD or is not working for
your very particular purposes, just try something that really works
for you!

If you're still there, here is my solution to your problem: PLAY WITH
VMD. There is no other way to master the program. There is a lot you
can get from it, believe me. But you'll say "I don't have time to mess
around", and it's completely valid. VMD, as all programs, will do what
you want it to do. If you are a little bit more curious and check out
previous postings, I'm pretty sure you'll find a good solution to your
problem. You moved your molecule, asked vmd to save a state and it
didn't do it? Then maybe you need to save your new coordinates first.
The trick is: YOU HAVE TO BE VERY EXPLICIT -The programs are dumb, you
need to make them work for your needs!

One more thing: as a scientist, you have to be patient. Very patient.
So don't give up, try it again and good luck!

Michel

2007/2/8, wolfinbm_at_uci.edu <wolfinbm_at_uci.edu>:
> Hello
> I am having extreme difficulty doing what are seemingly the most basic
> things in VMD. For example, I have two PET molecules that I have moved to
> start the membrane. It seems that I should just be able to save the state
> and save all the work I have done. But this is not how it works. When I
> go to re-load, the coordinates are not saved (yes I sent a message to this
> effect before, but the only responses I got seemed extremely cryptic, much
> like everything else I try to do in VMD). I am not trying to be rude or
> insult the programmers of VMD (it seems like a very powerful program if
> one can get it to work!), but I really do need some help. I have have
> spent dozens (or maybe hundreds) of hours trying to do what are
> intuitively very simple things (i.e., making a polymer from a monomer, and
> saving multiple molecules) and gotten absolutely nowhere. I would just
> give up and say it's my stupidity, but I've had no problem with many other
> challenging endeavors (I managed an 800 [highest score] on the GRE math,
> 680 on the verbal, and 740 on the physics, and I am a senior physics
> major). Could someone please give me some pointers, outside of "read the
> tutorials?"
>
> Any help is sincerely and greatly appreciated.
> Thanks,
> Matt Wolfinbarger
>
>
>