[gmx-developers] NMR refinement

santhu kumar mesanthu at gmail.com
Sun Jan 13 04:26:51 CET 2013

Hello all,

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

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

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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