Re: [gmx-developers] NMR refinement
hess at kth.se
Sun Jan 13 08:57:06 CET 2013
RDCs, including ensmeble averaging are implemented through what's called orientation restraints.
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From: "santhu kumar" <mesanthu at gmail.com>
To: <gmx-developers at gromacs.org>
Subject: [gmx-developers] NMR refinement
Date: Sun, Jan 13, 2013 04:26
I am trying to reproduce an NMR refinement protocol detailed in EROS, "Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution".
The method talks about 2 types of ensemble restraints :1). NOE restraints as distance restraints and the NOE violation is computed as a average value over 8 conformations which are simultaneously refined. (This could be achieved with -multi and distance restraint).
2). RDC restraint : compute the RDC from the ensemble of 8 conformation and the experimental value. And add the restraint for the corresponding atomic pair. Or briefly a force addition to the atomic pair involved, eg : N and HN.
NOE distance restraints are straight forward in Gromacs as the code itself has provisions for it. But the RDC's are a bit complex and I did not find a code/mail which implemented it. I would like to know your view about the way to proceed.
1). Should I change the code itself? Write a custom code which would be called before every integration step and adds a force vector to the existing force vector? What would be ideal location for this code? Though I found a few mails regarding these, those seem to be very specific to the application. (I might be wrong too). Since -multi would be always be there as a running option, any pointers on how would that affect the implementation.
2). Is there any way, I could write a tabulated force file in which I would provide only the force (Fx, Fy, Fz) for every atom, which could be directly added to the existing force vector. That way, I could write a script which would run the gromacs mdrun for one step and read the file to update the forces and repeat for certain number of steps. I am thinking of python wrappers of gromacs for the scripting. (This could slow down the system considerably but my simulations would not be too long, at this point this is not a concern).
I looked a solution from the mailing list but could not find one. ThanksSanthosh
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