From: David Huggins (djh210_at_cam.ac.uk)
Date: Tue Apr 26 2016 - 09:28:15 CDT
Thanks Brian,
I want no interactions between chains B and C and no interactions
between chains D and E. When I do this using alchemify I need to put B
and D in alchemical group 1 and C and E in alchemical group 2 and thus
the interactions between chains B and E and C and D are also switched
off. This seems to cause NAMD to die.
Thanks Jerome,
This seems to work when I hand make a PSF file with the NNBs, so I
will rewrite alchemify.
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/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On 25 April 2016 at 17:31, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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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