[gmx-users] Re: Constraints between multiple molecules

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 5 13:12:05 CEST 2010

Thomas Schlesier wrote:
> 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 
> constraints.
> 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.

Or just re-create the topology with pdb2gmx -merge.


> Greetings
> Thomas
>> 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.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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