Re: Alchemify Possibilities

From: Brian Radak (bradak_at_anl.gov)
Date: Mon Apr 25 2016 - 11:15:19 CDT

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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