<span style="font-family: Arial;">Hi,<br><br>RDCs, including ensmeble averaging are implemented through what's called orientation restraints.<br><br>Cheers,<br><br>Berk<br><br><br><div id="htc_header" style="">----- Reply message -----<br>From: "santhu kumar" <mesanthu@gmail.com><br>To: <gmx-developers@gromacs.org><br>Subject: [gmx-developers] NMR refinement<br>Date: Sun, Jan 13, 2013 04:26<br><br></div></span><br><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">Hello all,<br><div class="gmail_quote"><div><br></div><div>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". </div>
<div>The method talks about 2 types of ensemble restraints :</div><div>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).</div>
<div>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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>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). </div>
<div><br></div><div>I looked a solution from the mailing list but could not find one. </div><div>Thanks</div><div>Santhosh</div>
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