Dear All, This is a general query regarding solvation of peptide in urea-water. My method is to place the peptide in the box first, add urea molecules using g_genbox and then solvate it using water molecules to maintain a desired concentration. There can be two approaches to this: 1) I can keep no.of water molecules constant and increase the urea molecules like 15,30,45 and so on. Here total number of particles will not remain constant
2) I can keep total number of particles constant. Say I have 999 water molecules initially and then I add 15 molecules of urea and the system becomes like 985water-15urea and then subsequently 969water-30urea. But wouln't the effect on peptide hydration will be biased in terms of which is actually causing decrease/increase in hydrogen bonding with water: decrease of water or addition of cosolute? In many papers, I have seen that the no.of water molecules decreases with addition of cosolute. Is there any drawback if I use the first method? Yours sincerely Apramita -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
