[gmx-users] g_cluster: treating identical molecules as interchangeable

[Erik Marklund]

Hi,

If you have a small number of identical molecules you can achieve something along those lines by creating a trajectory where, say, the first half is the coordinates of the first molecule and the second half is the coordinated of the second molecule (for the case of two identical molecules). No matter the way you go about it there is no avoiding getting some artificial contribution to the transition probabilities between clusters.

Erik

Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 13 May 2014, at 14:57, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
> 
> I would expect there is no way to do this with g_cluster. g_cluster -h
> should mention it if it did exist. The only way to implement it is to
> iterate over all permutations of equivalent molecules. That's doable, but
> it would have to have been implemented deliberately.
> 
> Mark
> 
> 
> On Tue, May 13, 2014 at 1:27 PM, Gil Rutter <g.o.rutter at warwick.ac.uk>wrote:
> 
>> Hi all,
>> 
>> In a simulation of, say, 2 units of the same molecule, it would be useful
>> if g_cluster could treat the two molecules as being interchangeable.
>> 
>> For example, if molecule A has three atoms at coordinates C1, C2 and C3,
>> and identical molecule B has three atoms at coordinates C4, C5 and C6, this
>> frame would be clustered with a second frame in which molecule B is at C1,
>> C2 and C3 and molecule A is at C4, C5 and C6. (Indeed, in this case the
>> RMSD would be 0.)
>> 
>> Hopefully that makes sense. Is there any way to achieve this in g_cluster?
>> 
>> Best regards,
>> 
>> Gil Rutter
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