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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Aug 30 2012 - 09:47:47 CDT

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Hi,

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 [mailto:marletm8_at_gmail.com]
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
simulation)

Thanks again,

Best regards,

Marlet

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