[gmx-users] Molecular dynamics hydration site

babu gokul bbgkl at yahoo.co.in
Sat Nov 13 08:07:53 CET 2010

Dear all 

I read the above linked paper about the to find a molecular density  hydration 
map it says 

"For each step of the MD trajectory, the protein was fitted to a consistent 
frame of reference." 

I did this by using trjconv i have fitted the protein in my trajectory

" Next, the same  transformation was applied to the water molecule coordinates, 
taking the periodic boundaries into account."

I did the same by using trjconv by using the trajectory i have obtained from the 
previous step

" The coordinates of the water oxygen  atoms were then mapped onto the 
three-dimensional rectangular grid with a 0.5 Å grid step, producing an average 
three-dimensional number density distribution. The particular choice of the grid 
step is a compromise between the uncertainty in location of the density features 
and the statistical error in the local density value that arises due to a lower 
number of counts in each  grid cell. At the chosen grid step every cell in the 
regions corresponding to bulk solvent would have at least 50 counts over the 
entire trajectory. The density map was smoothed by averaging the value of each 
cell with six of its nearest neighbors before further manipulations. "

I did the above step by using GridCount tool i got a grid.dat then i transformed 
the that to a vmd readable format density map.

but when i visualize the file in vmd i got a lot of density over the corner but 
i was not able to visualize the it near the protein molecule as  given in the 
above mentioned paper 

could anyone helpme in this regard how to do the same analysis in gromacs.

Thanks in advance 

E R Azhagiya singam 

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