Re: [ESPResSo] pbc wrap & folded/unfolded coordinates

[Tristan Bereau]

Hi Salvador,

 - About the VMD error message: edit the file ESPRESSO_DIRECTORY/scripts/vmd_plg.tcl and, around line 136, replace

lassign $v1 x y z q

lassign $v2 u v w p

return [expr $x*$u + $y*$v + $z*$w + $p*$q]

by

lassign $v1 x y z

lassign $v2 u v w

return [expr $x*$u + $y*$v + $z*$w]

There's probably a better way than hacking it like this, but I've never gotten into trouble for doing that!

 - For movie making, have you tried using the plugin: Extensions > Analysis > RMSD Trajectory Tool and then clicking on "Align"? 

 - As for your analysis, I would probably do some scripting that calculates the center of the vesicle, and then for each lipid determine which periodic image is closest to that center, and create a new PDB file out of that. You can then perform all your analysis routines.

Best,

Tristan

On Jun 1, 2010, at 18:46 , Salvador Herrera Velarde wrote:

Hi Olaf,

Thanks a lot for your answer in the vmd mail-list. I am moving my question to ESPResSo list beacuse I think is also
related with ESPResSo.

First of all, I would like to mention that I using linux (Centos) and when I launch vmd-1.8.7, inmediatly I receive the following message:
Error updating the cell information
missing operand at address@hidden
in _expression_ "address@hidden"

Regarding my problem, I have a series of pdb files generated with ESPResSo (using mbtools). The command that I used was:
writepdbfoldtopo "$outputdir/$ident.vmd[format %04d $j].pdb"

I need to create a movie using these pdbs files, however at some point of the simulation my vesicle move away from
the center and it is splitted due to periodic boundary conditions. Besides, I need to do some analysis with these pdbs files
(need to calculate gr, Rg... etc), but due to the splitting of the molecules I am facing some troubles to calculate correctly such observables.
What are the best options to make the movie without splitting and to calculate the observables?

Thanks a lot.

Best regards,

Salvador
_______________________________________________
ESPResSo mailing list
address@hidden
https://fias.uni-frankfurt.de/mailman/listinfo/espresso