Hi, you could find the number of waters around each using g_order. Then you would need to have a small script to combine the two lists to find only the ones close to both.
Roland On Sat, Oct 23, 2010 at 7:47 AM, leila karami <[email protected]>wrote: > Hi gromacs users > > Since I study dynamic of interfacial water molecules between protein and > dna, I want to know, is there any keyword in gromacs to obtain number of > interfacial water molecules between protein and dna as a function of > simulation time? Is there any way which water molecules put in interface > between protein and dna? > > any help will highly appreciated. > > > > > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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