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).
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. Any susggestions on how the pull code can be utilized is very much appreciated! Warren On Tue, Apr 14, 2009 at 2:14 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > warren deng wrote: > >> Hi Gromacs users, >> >> 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. >> So I am wondering whether it is possible to create distance restraint >> between two molecule types in Gromacs? >> > > 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. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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