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Add pore waters by CHARMM-GUI
#33619 03/25/14 04:29 PM
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Hello everyone!

Hope you're enjoying the week! I have some questions about how CHARMM-GUI adds pore waters. I attach the input file below. My questions are:

1) In "Step3: Dynamics", what was the Langevin Dynamics designed for?

2) In "Step3: Dynamics", CHARMM-GUI adds a series of MMFP restraints to waters. Can anyone explain the logic of them?

3) In "Step3: Dynamics", why does the script use a temperature of 5000.0 K for Langevin dynamics?

4) What was "Step3: Individual Comparison" designed for?

Thanks in advance.

Best

Attached Files
step2.1_pore.txt (6.64 KB, 295 downloads)
Last edited by shane yue; 03/25/14 05:16 PM.

Zhi (Shane) Yue
Department of Chemistry
University of Chicago
Re: Add pore waters by CHARMM-GUI
shane yue #33628 03/25/14 05:37 PM
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We defined pore region as empty space where lateral diffusion of water is restricted by the surrounding protein. To find such space, we solvated water and capped horizontal diffusion of water using MMFP at the top and the bottom of the lipid bilayer (Z = +20/-20). After that, we ran short Langevin dynamics at very high temperature, so that any other that are not confined by the protein will diffuse away, followed by removal of water molecules that are not bound by protein extent. Finally, some water may stay close to the protein exterior. That is the "individual comparison" step designed for.

Re: Add pore waters by CHARMM-GUI
Sunhwan #33630 03/25/14 06:19 PM
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Hi Sunhwan,

Thanks for your explanation. It helps a lot. Nice day!

Best


Zhi (Shane) Yue
Department of Chemistry
University of Chicago

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