AW: simulation:protein,ligand,lipid,water and ions

From: Norman Geist (
Date: Thu Aug 30 2012 - 09:47:47 CDT



well what you see is IMHO just a shift of your protein through the periodic
box. And as the box is periodic it doesn't matter where your protein is
located in the box. Check the wrap command I posted, this will center the
protein in the box.


vmd> pbc wrap -all -compound res -center com -centersel protein


Norman Geist.


Von: Marlet Martinez []
Gesendet: Donnerstag, 30. August 2012 16:39
An: Norman Geist
Betreff: simulation:protein,ligand,lipid,water and ions


Dear Dr. Geist,

Thank you so much for your response. Yes, I have used wrapALL amd wrapWater
commands in every configuration file of the simulation.

As you can see in my image, water molecules tend to move downward and this
happens after I run the fourth configuration file (at the end of the

Thanks again,

Best regards,


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