From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Aug 31 2012 - 00:47:21 CDT
Hi,
of course VMD can't wrap your system, as psf and pdb both does not contain
the box size information. If you would have loaded the dcd, it would have
worked.
You can easily set the box with:
vmd> pbc set {x y z} [-all]
The -all parameter is optional and will cause the box to be set for all
frames, not only the current.
and then do:
vmd> pbc wrap -all -compound res -center com -centersel protein
And yes, the picture of the system you showed is wrapped, and you could just
go on with this structure. Please inform yourself about the periodic
boundary condition to understand, that is doesn't matter where your protein
located, and if the water is below or over the protein.
If you use the wrap command on your dcd trajectory, you will see maybe.
Norman Geist.
Von: Marlet Martinez [mailto:marletm8_at_gmail.com]
Gesendet: Freitag, 31. August 2012 02:55
An: Norman Geist
Betreff: Re: namd-l: AW: simulation:protein,ligand,lipid,water and ions
Dear Dr. Geist,
It is me again, sorry I meant I opened my .psf file and .dcd file in the
vmd. and by doing this I got a warning:
pbcwrap: selection "protein" is empty!
measure center: bad weight sum, would cause divide by zero
It is weird because I used in every configuration files the comman:
wrapWater on and wrapAll on (I attach the last conf file as an example)
Thank you so much for your attention and your patience,
Marlet
2012/8/30 Norman Geist <norman.geist_at_uni-greifswald.de>
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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