Dear Justin, If possible, can you some explain "net attraction"?
Best regards 2011/9/22 Justin A. Lemkul <[email protected]> > > > ahmet yıldırım wrote: > >> Dear users, >> >> 1.) During the simulation the mean potential energy is minus (-) value. >> What does this mean? Why minus? >> > > Net attraction. > > > 2.) let's say, Interface/Buried Surace Area (ISA) between protein and >> ligand was calculated and hydrophobic ISA obtained greater than hydrophilic >> ISA. What does this mean? >> >> > That, as you might expect, hydrophobic groups are shielded from the solvent > to a greater extent than polar groups. > > -Justin > > > No one is my special advisor but If you help me, I will be happy. >> >> Thanks in advance >> >> -- >> Ahmet YILDIRIM >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM
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