VMD-L Mailing List

From: Kailee (kaileeamber_at_googlemail.com)
Date: Wed Mar 21 2007 - 09:14:33 CDT

Dear all VMD users,

I have done a 1ns md simulation (seperated into 10 calculations) of hydrogen
molecule diffusion into a big protein using LES method in AMBER. And I have
made 1000 LES copies of the hydrogen molecule. Now I want to analyse the
trajectory files (especially the hydrogen molecule pathways). So I loaded
all the 10 trajectories files one by one into VMD. And now my questions are:

1) I tried to superimpose the hydrogen molecule trajectories, what I did
was: select the representation of hydrogen molecule, and in the
'trajectory-> draw multiple frames', I changed 'now' to '0:', is it the
right way to do this?

2) Because I don't want to look at all the hydrogens but only hydrogens
within a certain distance of the protein center, so in the 'selections', I
typed 'resname H2 and (within 50 of name FE)', as I want to look at the
hydrogen molecules within 50A of the Fe atom. However, it turned out that
some hydrogens which are very obvious not within 50A of Fe still there. I am
thinking it might because of the periodic boundary problem that some
hydrogens flied out of the primary box and I should reimage them back to the
central box. Is it right? And if so, how can I do it in VMD?

3) And also when I superimposed the hydrogen trajecotries, the
representation of the protein residues became really not clear, I tried
different draw styles but still can't find out how to do it. Actually I have
attached a picture that I copied from a paper, what I want to do is almost
exactly what he did, but just using different protein molecule, can anyone
who is familiar with VMD guide me how to make a picture like that please?

Thanks very much for any suggestions!
With my best regards,

Kailee

When I load the trajectories into VMD, I found that there are many hydrogen
molecules flied out of the primary box, can I ask how can I reimage them
back to the central box? what is the difference in doing so between the
simulations with and without LES method?