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

From: Tristan Bereau
Subject: Re: [ESPResSo] pbc wrap & folded/unfolded coordinates
Date: Tue, 1 Jun 2010 22:16:26 -0400

By the way, if you're using a DPD thermostat, I think that ESPResSo offers a routine that stops the center of mass motion of the system. I don't know if that's implemented in mbtools, you might have to add it.


On Jun 1, 2010, at 22:09 , Tristan Bereau wrote:

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]


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.


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,

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