[AMBER] Umbrella sampling coordinate question

From: Rajesh Raju <rajesh.raju.mail.chem.tamu.edu>
Date: Tue, 08 Mar 2011 17:21:36 -0600

Dear Amber users,

I am planning to do an umbrella sampling on one of the receptor
molecule. I used the distance between the center of masses of the
receptor and ligand molecule as constraint. My doubts are:

[1] Do I need to make different coordinate files for the complex,
corresponding to the distance between the center of masses of the two
molecules? or Can I use the same coordinate file for all individual
simulations of the different windows?

[2] changing the distance variable in the 'DISANG=dist.dat' file to
different distance values corresponding to different windows, and keep
the same coordinate files with center of masses of two molecules close
to zero, would be the same effect as that of the doing different
window simulations, making new coord files corresponding to the
umbrella sampling distance.

So far I proceeded with the second approach:

I made the new coordinates corresponding to different R variables from
0.5 to 10 ..20 windows. and made parameter and coordinate files for
the individual windows..The number of water molecules are slightly

Which is the best way?


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Received on Tue Mar 08 2011 - 15:30:04 PST
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