From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Apr 25 2016 - 11:31:32 CDT
Hi Dave,
The alchemy code in NAMD, and alchemify, are designed for just two groups
in mind. If you are familiar with C programming, I believe you can achieve
the desired result with minor modifications of alchemify.
Jerome
On 25 April 2016 at 18:15, Brian Radak <bradak_at_anl.gov> wrote:
> The standalone alchemify program is, I believe, largely deprecated. All of
> the PSF cleanup can now be done at startup inside NAMD. You do, however,
> still have to tag your groups in a PDB file (using 0, 1, -1 in the bfactor
> column by default).
>
> As for your specific case, do you mean that you want B and D to be in
> alchemical group 1 and C and E to be in alchemical group 2? Or do you want
> 4 separate alchemical groups? NAMD does not currently support the latter.
>
> Brian
>
>
> On 04/25/2016 11:03 AM, David Huggins wrote:
>
>> Hello all,
>>
>> I am having a little trouble with the alchemify tool
>>
>> It is working with no problem if I switch off interactions between
>> chains B and C, but I would like it to switch off interactions between
>> chains D and E as well as between chains B and C. Is this possible
>> with alchemify? When I try it, the simulations always die immediately
>> with a "Low global exclusion count"
>>
>> Thanks,
>>
>> 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/
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
>
>
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