[gmx-users] End to end fixing

[Seera Suryanarayana]

Dear Gromacs users,

I have one protein which has the topological domain with two trans membrane
domains. I would like to simulate the topological domain present in the
cytosol. But here I can't do simulations as normals proteins. Because as
the topological domain has trans membrane domains both sides, which
suggests me that the ends should be fixed during simulations. The question
is "How do we fix the ends? means what should be the distance between the
end? To solve this question I have looked into the NMR structure of the
protein in PDB. The protein has 20 different conformational states. I
checked the distance between the N'-terminal C-alpha and C'-terminal
C-alpha. All the conformations showing large variance. How could I solve
end-to-end fixing? Kindly tell me what can I do.

Thanks in advane

Surya
Graduate student
India.