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[ESPResSo] pbc wrap & folded/unfolded coordinates

From: Salvador Herrera Velarde
Subject: [ESPResSo] pbc wrap & folded/unfolded coordinates
Date: Tue, 01 Jun 2010 17:46:32 -0500

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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