From: David Huggins (djh210_at_cam.ac.uk)
Date: Tue Apr 25 2017 - 14:10:06 CDT
Thanks Jerome,
Please can you clarify what you mean? Do you suggest increasing the
cutoff or using a later version of NAMD?
Best wishes,
Dave
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr David J. Huggins
University of Cambridge
Department of Chemistry
Lensfield Rd
Cambridge
CB2 1EW
United Kingdom
Phone: +44 (0)1223 763854
Email: djh210_at_cam.ac.uk
Web: http://huggins-lab.tcm.phy.cam.ac.uk/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On 28 May 2016 at 05:00, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Dear Dave,
>
> I was reminded today that explicitly excluded atoms are expected to lie
> within the cutoff distance. Those exclusions are not required (anymore) in
> standard FEP runs because those atoms belong to separate partitions. That
> might be the way to go for your needs.
>
> Best,
> Jerome
>
> On 27 May 2016 at 22:21, David Huggins <djh210_at_cam.ac.uk> wrote:
>>
>> Dear All,
>>
>> I am trying to implement a NAMD version of the separated topologies
>> method from "Separated topologies—A method for relative binding free
>> energy calculations using orientational restraints".
>>
>> I have used alchemify to switch off interactions between two ligands
>> in a protein binding site and the protocol requires me to run dynamics
>> where both ligands are fully coupled to the system (though not to each
>> other).
>>
>> However, the resulting simulations always exit early with a "Low
>> global exclusion count". I have tried gentle heating and reduced
>> timesteps but neither works.
>>
>> Does anyone have any experience of running simulations where two fully
>> coupled species are overlapping and have no mutual interactions?
>>
>> Best wishes,
>>
>> Dave
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> Dr David J. Huggins
>> MRC New Investigator
>> Theory of Condensed Matter Group
>> Cavendish Laboratory
>> JJ Thomson Avenue
>> Cambridge, CB3 0HE
>> United Kingdom
>>
>> Phone: +44 (0)1223 764164
>> Fax: +44 (0)1223 337356
>> Email: djh210_at_cam.ac.uk
>> Web: http://www.tcm.phy.cam.ac.uk/~djh210/
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>
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