[gmx-developers] Umbrella code extension

Berk Hess hess at kth.se
Wed Feb 12 15:08:26 CET 2014


This indeed looks like a flat-bottomed restraint potential. I had 
proposed that addition to the pull code for 5.0 in a request for 
feedback, which I also posted to the developers list. But since I didn't 
receive any response on this point I didn't implement it. Also because a 
general flat bottomed potential needs an extra (distance) parameter. It 
seems like your potential would not need an extra parameter (it should 
equal a flat bottomed potential with lower limit 0). Since it's too late 
for 5.0, I would propose to implement the flat bottomed potential for 5.1.



On 02/12/2014 02:31 PM, Shirts, Michael (mrs5pt) wrote:
> 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
> molecule.
> 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?
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
> On 2/12/14, 8:20 AM, "Sabine Reisser" <sabine.reisser at kit.edu> wrote:
>> Hello,
>> 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
>> process.
>> 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)
>> Germany
>> -- 
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