[gmx-users] Position restraints while performing pulling run for Umbrella sampling

ARNAB MUKHERJEE arnabmukherjee249 at gmail.com
Thu Dec 20 20:12:49 CET 2018


I am intending to perform pulling run for umbrella sampling, on my coarse
grained DNA protein system where I have a bundle containing 20 DNAs and
proteins. I want to pull 1 DNA out of this bundle to perform Umbrella
Sampling. I was going through this tutorial
So since I want to pull 1 DNA out of the bundle, I would like to position
restrain the atoms of the other 19 DNAs. But as mentioned here
http://www.gromacs.org/Documentation/How-tos/Position_Restraints, I need to
add the position restraints under the molecule type of DNA, in my .top
file, but then shouldn't it restrain the atoms of all the 20 DNAs? How can
I restrain the atoms of other 19 DNAs, except the DNA that I am pulling?

I would highly appreciate any help.

Thank you very much,



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