[gmx-users] NMR refinement

santhu kumar mesanthu at gmail.com
Fri Jan 11 07:14:34 CET 2013

Hello all,

I am trying to reproduce an NMR refinement protocol detailed in EROS,
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. *

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