[gmx-users] Molecular dynamics hydration site

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 13 12:09:11 CET 2010

On 13/11/2010 6:07 PM, babu gokul wrote:
> Dear all
> "http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B94RW-4TYB1FX-K-1&_cdi=56421&_user=1245000&_pii=S0006349500765337&_coverDate=12/31/2000&_sk=%23TOC%2356421%232000%23999209993%23703217%23FLA%23display%23Volume_79,_Issue_6,_Pages_2783-3354_(December_2000)%23tagged%23Volume%23first%3D79%23Issue%23first%3D6%23date%23(December_2000)%23&view=c&_gw=y&wchp=dGLbVlb-zSkWb&md5=4e66a17da4627571bfd990beae45d486&ie=/sdarticle.pdf 
> <http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B94RW-4TYB1FX-K-1&_cdi=56421&_user=1245000&_pii=S0006349500765337&_coverDate=12/31/2000&_sk=%23TOC%2356421%232000%23999209993%23703217%23FLA%23display%23Volume_79,_Issue_6,_Pages_2783-3354_%28December_2000%29%23tagged%23Volume%23first%3D79%23Issue%23first%3D6%23date%23%28December_2000%29%23&view=c&_gw=y&wchp=dGLbVlb-zSkWb&md5=4e66a17da4627571bfd990beae45d486&ie=/sdarticle.pdf>"
> 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

The simplest thing that can go wrong is that your visualization of the 
density is based on an unsuitable range of density. However, you'll have 
to consult the documentation of GridCount and VMD - you're not very 
likely to get help for those on a GROMACS mailing list.

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

g_density can calculate 3D number density histograms, however there 
might be a bunch of work to (say) visualize that histogram in (say) VMD 
overlaying your system, or such.

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