[gmx-developers] Umbrella code extension

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Wed Feb 12 14:58:10 CET 2014

Hi, Sabine-

So, this looks like the distance restraint potential (bond function 10) in
section 4.3.4 of the manual that matches this potential function.  Right
now, this potential can only be applied.  However, there is a planned fix
for 5.0 that will include the ability to add all bonded interactions in
between arbitrary atoms in the system, even if they are not in the same

I BELIEVE there is an extension to the pull code that would allow general
bonded potentials to be used between COMs of index groups as well but I'm
not as certain about that.

I think that these planned changes will capture the functionality that you
are describing.  Is that correct?


Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

On 2/12/14, 8:20 AM, "Sabine Reisser" <sabine.reisser at kit.edu> wrote:

>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
>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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