Re: Method for solvation of protein

From: Dong Luo (us917_at_yahoo.com)
Date: Tue Oct 22 2013 - 10:57:17 CDT

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Hi Xingcheng,

If you know programming, you can read the solvate plugin's source code located at VMD_install_dir/plugins/noarch/tcl/solvate1.5. Basically it replicates the pre-equilibrated water box (9261 H2O molecules, wat.psf, wat.pdb are at same folder) to required size, then put in the protein molecule, and finally remove overlapped H2O.

Dong

On Monday, October 21, 2013 4:50 PM, Xingcheng Lin <linxingcheng50311_at_gmail.com> wrote:
 
Hi everyone,

I have got a question on the solvation of protein in VMD.

In the solvate plugin, does the VMD patch the space with somehow pre-equilibriated water or just randomly put water into the box until no water molecule can be filled in?

Thank you,
Arrow

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