[gmx-developers] Umbrella code extension / flat bottom potential

[David van der Spoel]

On 2014-02-12 15:24, Sabine Reisser wrote:
> Hi,
>
>   "It seems like your potential would not need an extra parameter (it
> should
> equal a flat bottomed potential with lower limit 0)."
>
A flat bottom potential is already in the code and we have used it 
extensively. Jochen Hub has implemented it.

> Yes, this is exactly what I mean.
>
> Thanks & cheers
> Sabine
>
>
>
> 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
>>>>
>>>>
>>>>
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>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se