[gmx-developers] Umbrella code extension

Sabine Reisser sabine.reisser at kit.edu
Wed Feb 12 14:20:32 CET 2014


I have implemented an extension to the existing umbrella code in Gromacs 
version 4.6.3. It is a semiharmonic potential which sets a maximum 
distance between two index groups. When this distance is trespassed, a 
force kicks in and bounces the pull group back, when the distance is 
below the threshold, motions are completely unrestrained. I use this 
code to simulate pores of antimicrobial peptides, to keep the peptides 
in close vicinity without actually interfering with the pore formation 
The code can also be used to make sure several peptides bind to the same 
side of a membrane or in ligand-binding simulations.
The relevant part of the extended code is no longer than 10 lines, but I 
naturally had to change other files in order to read the modified input 
from the mdp files, too. Affected binaries are mdrun and grompp.
Instead of providing this singular modified Gromacs 4.6.3 as a tarball 
for downloading, I would like to get this extension into the official 
release so that it is maintained also in future releases.

What is the procedure to achieve this or who is the best person to address?

With best regards

Sabine Reißer

Dipl. phys. Sabine Reißer
Theoretical Chemical Biology
Institute for Physical Chemistry
Karlsruhe Institute for Technology (KIT)

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