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

[Mark Abraham]

It's been in master branch for about a year :-)

Mark


On Wed, Feb 12, 2014 at 8:20 PM, Berk Hess <hess at kth.se> wrote:

> On 02/12/2014 04:55 PM, David van der Spoel wrote:
>
>> 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.
>>
> Not in the main distribution.
>
> Cheers,
>
> Berk
>
>
>>  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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>>>>>
>>>
>>
>>
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