[gmx-users] Re: Constraints between multiple molecules

Thomas Schlesier schlesi at uni-mainz.de
Thu Aug 5 12:55:18 CEST 2010

One thing which you could do is to write your three proteins into one 
molecule definition (if you use .itp files, then make one .itp for all 
three). Then at the end of the molecule definition you can add the 
To merge the three proteins is rather easy but cumbersome, you must 
shift all the atom numbers of the second and third protein. So if each 
protein would have 100 atoms, protein2 would start with atom 101. 
depending how big your proteins are it could be better to write a script 
which merges the three proteins instead of doing it by hand.


> Hi everyone. ?I'm doing a simulation of a protein aggregate with 3 proteins. ?Ideally, I would like to constrain the distance between the center of mass of peptide 1 and the COM of peptide 2, and also constrain the distance between the combined COM of peptides 1 & 2, with the COM of peptide 3. ?The pull code only allows constraints between the reference group and other groups, as far as I know.
> Using constraints in the topology only allows constraints between atoms, not COM's. ?This is not ideal for me, but might be acceptable. ?However, constraints are only allowed within a single molecule.
> Does anyone know how to deal with this problem? ?Thanks a lot.

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