[gmx-users] End to end fixing

Mark Abraham mark.j.abraham at gmail.com
Mon May 25 18:49:50 CEST 2015


Unless the time scale of the motion in which you are interested is orders
of magnitude faster than the motions of the transmembrane domains, and
there is no reason to believe the proximity of the membrane is a factor,
then it sounds like simulating the solvated domain in isolation would have
no connection with reality.


On Mon, May 25, 2015 at 7:25 AM Seera Suryanarayana <palusoori at gmail.com>

> 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.
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