[gmx-developers] Umbrella code extension

Sabine Reisser sabine.reisser at kit.edu
Wed Feb 12 15:24:59 CET 2014


  "It seems like your potential would not need an extra parameter (it should
equal a flat bottomed potential with lower limit 0)."

Yes, this is exactly what I mean.

Thanks & cheers

On 02/12/2014 03:08 PM, Berk Hess wrote:
> Hi,
> 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.
> Cheers,
> Berk
> 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
>>> -- 
>>> Gromacs Developers mailing list
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
>>> posting!
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>>> or send a mail to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list