<div>Hi Jochen,</div>
<div> </div>
<div>Thanks a lot for the information, I appreciate. I will merge the two proteins into a single moleculetype and apply the distance restraint, as you suggested. Although I could try use the pull code, I am not sure if they interfere with free energ (lambda) code which I am also using.</div>
<div> </div>
<div>With best wishes,</div>
<div> </div>
<div>Warren<br><br></div>
<div class="gmail_quote">On Tue, Apr 14, 2009 at 6:59 PM, Jochen Hub <span dir="ltr"><<a href="mailto:jhub@gwdg.de" target="_blank">jhub@gwdg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Warren,<br><br>if you want to use distance restraints, the two proteins must be in the<br>same gromacs "molecule". AFAIK, it is impossible to use distance<br>
restraints between atoms of different molecules. Altermatively, you may<br>want to consider bonds of type 6 (not subject to lincs).<br><br>pdb2gmx -merge is useful to create the topology of a "molecule" that<br>
actually contains 2 proteins.<br><br>If the two proteins must be in different gromacs "molecules", you would<br>have to use the pull code.<br><br>Best,<br>Jochen<br>
<div>
<div></div>
<div><br><br>warren deng wrote:<br>> Hi Gromacs users,<br>><br>> In my simulation, I need to restrain distances between atoms on two protein<br>> molecules. But the Gromacs manual on NOE seems to imply that the atom<br>
> indices belong to the same molecule type.<br>><br>> So I am wondering whether it is possible to create distance restraint<br>> between two molecule types in Gromacs?<br>><br>> Many thanks,<br>><br>> Warren<br>
><br>><br>><br></div></div>> ------------------------------------------------------------------------<br>
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Dr. Jochen Hub<br>Max Planck Institute for Biophysical Chemistry<br>Computational biomolecular dynamics group<br>Am Fassberg 11<br>D-37077 Goettingen, Germany<br>Email: jhub[at]<a href="http://gwdg.de/" target="_blank">gwdg.de</a><br>
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