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

ARNAB MUKHERJEE arnabmukherjee249 at gmail.com
Fri Dec 21 15:01:45 CET 2018

Hello everyone,

I hope I have been able to write it clearly the problem I am facing. It
would be very helpful for me if someone can please guide me how to solve
this problem.

Thank you in advance,



On Thu, Dec 20, 2018 at 8:20 PM ARNAB MUKHERJEE <arnabmukherjee249 at gmail.com>

> Hi,
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html.
> 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,
> Regards,
> Arnab

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