From: Ropon-Palacios G. (biodano.geo_at_gmail.com)
Date: Tue Mar 16 2021 - 17:45:01 CDT
I have not had any rapprochement with tclBC, I don't know if you could give me an example that I can start with please.
On the other hand, I found in the example of colvar one called "02_aggregation.colvars.in", basically what I want is that the molecules (84 ligands placed around my protein at random), I don't know how to add, forming a cluster of itself, already I have a high number and many authors have mentioned this phenomenon. This script (02_aggregtion_colvars.in) that I found in the examples might help me.
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Date: Tuesday, March 16, 2021 at 5:01 PM
To: NAMD list <namd-l_at_ks.uiuc.edu>, David Hardy <dhardy_at_ks.uiuc.edu>
Cc: "ROPÓN-PALACIOS G." <biodano.geo_at_gmail.com>
Subject: Re: namd-l: Add repulsive potential with dummy atom
Hi Geo, the documentation at the Colvars website is a bit richer than what is included in the NAMD manual:
and there are specific examples listed on the top page:
However, there isn't likely to be an input file that is just ready to be reused, though, for several reasons:
1. There are details of your system that you didn't describe, but would be needed to prepare a good input.
2. The version of NAMD that you are using is important, as it affects the Colvars features available to you. In principle it is possible to build a more recent version of Colvars with older versions of NAMD, but this is not supported (meaning, it will likely work but taking more work on your part).
3. The Lennard-Jones potential is not present as a pre-compiled function for Colvars, although there are provisions to add custom functions at runtime listed in the Colvars doc.
4. If I understand correctly what Dave also understood, you have many pairs of molecules, which would mean a lot of variables that aren't really "collective".
Without resorting to advanced features/packages, why not simply pick one atom for each molecule, and apply forces between them with tclBC? It is slower than C++ code (like e.g. the force field functions from NAMD or the collective variables from Colvars), but it would be at least parallelized over nodes, and probably result in small overhead.
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