[gmx-developers] Lambda dynamics

[Carsten Kutzner]

Hi Michael,

On 09 Oct 2014, at 13:45, Shirts, Michael R. (mrs5pt) <mrs5pt at eservices.virginia.edu> wrote:

> Hi, all-
> 
> Carsten, I've been thinking about how to incorporate this into the current
> free energy structure.  It would be good to coordinate,
That sounds great!

> perhaps over
> redmine if that isn’t too public?
I think some time ago Thomas already left some comments on 
http://redmine.gromacs.org/issues/1332

Would this be the proper thread for further discussions?

> I think one if the issues with a lot of
> the free energy functionality being inconsistent and sometimes unreliable
> is that we’ve all been working piecemeal instead of coordinating.
Right. At some point we realized that PME is not very suited
when it comes to calculating multiple alternative states (since one needs
to do the communication-intense transforms for each alternative
charge grid) so we started to work on providing a fast multipole method
as an alternative to PME for such scenarios. This is in progress
and the topology/free energy treatment can be worked on more or less
independently. 

Regards,
  Carsten


> 
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
> 
> 
> 
> On 10/9/14, 7:14 AM, "Carsten Kutzner" <ckutzne at gwdg.de> wrote:
> 
>> Hi Erik,
>> 
>> On 09 Oct 2014, at 12:54, Erik Marklund <erik.marklund at chem.ox.ac.uk>
>> wrote:
>> 
>>> Dear developers,
>>> 
>>> I recall that someone had made an implementation of lambda dynamics in
>>> Gromacs. If anyone knows more about that please get in touch!
>> there is
>> 
>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114466/
>> 
>> for Gromacs 3.3. (see also http://www.mpibpc.mpg.de/grubmueller/constpH),
>> which is maintained by Serena Donnini.
>> 
>> We are working on a more general and more scalable version but that will
>> need some more
>> time before it is ready.
>> 
>> Carsten
>> 
>> 
>>> 
>>> Kind regards,
>>> Erik
>>> 
>>> 
>>> Erik Marklund, PhD
>>> Postdoctoral Research Fellow, JRF
>>> 
>>> Department of Chemistry
>>> Physical & Theoretical Chemistry Laboratory
>>> University of Oxford
>>> South Parks Road
>>> Oxford
>>> OX1 3QZ
>>> 
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>> 
>> 
>> --
>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics
>> Am Fassberg 11, 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>> 
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> 


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa