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Re: [ESPResSo-users] Virtual sites and topology

From: Axel Arnold
Subject: Re: [ESPResSo-users] Virtual sites and topology
Date: Thu, 9 Apr 2015 21:11:04 +0200


Am 06.04.2015 um 17:26 schrieb Aleksei Kabedev <address@hidden>:
2) how the "analyze set topo_part_sync" works? I honestly tried to understand the principle from the code, but it is not trivial at all.

There are several positions in Espresso, where the topology is stored:

- the pretty historic “chain” topology that is only used in analysis ("analyze set chains"). You can’t use this for defining COM groups.

- the generic information stored in the global variable topology, which you set via “analyze set”.

- the mol_id that is attached to each particle.

The virtual sites code uses both last two information sources. More precisely, it uses the mol_id of the virtual particles to determine the particle group of which it should be the center of mass. The information in “topology” is then used to determine the particles that belong to this molecule. As you see, it is pretty vital that those two information sources are consistent; in particular, there needs to be a molecule in “topology” with id equal to the mol_id of each virtual particle.

As described in the users’ guide, you first define the topology using “analyze set {mol_id {member member …} …}”. Then you need to update the mol_ids of at least the virtual particles to match the topology. That can be achieved either manually, or by calling “analyze set topo_part_sync”, since the virtual particle should also be contained in the member list.

So, what topo_data_sync does is simply looping over all molecules, and then over all particles in this molecule in order to overwrite the particles mol_id with the molecules mol_id.

If you see strange mol_ids, that means that your topology definition is wrong. To see what is not working there, you would need to send us the output of “analyze set” and the particles’ mol_ids after topo_part_sync.


Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Phone: +49 711 685 67609

Axel Arnold
Martha-Schmidtmann-Str. 7
70374 Stuttgart, Germany
Email: address@hidden
Phone: +49 173 870 6659

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