[gmx-users] interfacial water molecules

[chris.neale at utoronto.ca]

Part 1: Dear users,

does anybody have a good method to calculate the number of water  
molecules in the first hydration shell of a macromolecule?

Part 2: Dear Leila,

My Oct 23 2010 comment was correct in intention and general ideas, but  
I was incorrect when I suggested that it would be easy to "use a tool  
like g_dist to count the number of waters within that distance".

I have recently been attempting to determine the number of water  
molecules in the first hydration shell of a macromolecule. During this  
process, I realized that none of the available tools (g_dist,  
g_mindist, g_rdf) are suitable to do this without either modifying  
them or doing substantial scripting like running them on a per-frame  
basis (although I'm using gromacs 4.0.7 and perhaps there are new  
tools in gromacs 4.5.3 but the -h options to those tools don't  
indicate anything obvious to me).

Sorry for any confusion,
Chris.

-- original message Sat Oct 23 15:18:56 CEST 2010 --

Leila,

you didn't specify what you want exactly, but often what people want
is the number of waters in the first hydration shell. To get this, you
calculate an RDF of water oxygen around protein heavy atoms and
identify the first minimum. Then use a tool like g_dist to count the
number of waters within that distance. Do this for DNA and protein
separately, and then you might see that the number of waters in the
first hydration shell of these macromolecules decreases when they bind.

Chris.

-- original message --

Hi gromacs users

Since I study dynamic of interfacial water molecules between protein and
dna, I want to know, is there any keyword in gromacs to obtain number of
interfacial water molecules between protein and dna as a function of
simulation time? Is there any way which water molecules put in interface
between protein and dna?

any help will highly appreciated.