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

[Berk Hess]

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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>>
>
>