<div>Thank you Mark. The problem is, in order to use the couple-moltype option for decoupling, I want to keep the two proteins in separate moleculetype(s). </div>
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<div>Now I noted that Gromacs has a pull option for doing umbrella sampling, but I don't know how it might be used to apply distance restraint between two atoms belonging to two molecules. </div>
<div> </div>
<div>Any susggestions on how the pull code can be utilized is very much appreciated!</div>
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<div>Warren</div>
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<div class="gmail_quote">On Tue, Apr 14, 2009 at 2:14 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div class="h5">warren deng wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Gromacs users,<br><br>In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type.<br>
So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs?<br></blockquote><br></div></div>Indeed. You will need to create a moleculetype that contains both/all the molecules of interest. Note that atom numbers within a moleculetype must be unique.<br>
<br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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