Hi, Naturally such differences in system preparation are inevitable, and can be seen before any expensive simulation runs. So the absolute energies are different for different systems, but fortunately there was little to no value in comparing them even when they are formally comparable. However estimates of quantities based on energy differences, such as relative free energies of binding can be usefully made.
Mark On Sat., 20 Apr. 2019, 14:17 neelam wafa, <[email protected]> wrote: > Hi! > Dear Sir Justin. > I have run 5 ns simulations of two different enzymes in unbound form and in > complex with 4 different inhibitors each. Now when I compare the data I see > different number of solvent molecules added in each case( solvent being > water) enzyme 1 has +1 charge and neutrallized with one chloride ion while > enzyme 2 has -7 charge and neutralized with 7 sodium ions. the number > solvent molecules added are followings. > Enzyme 1 enzyme 2 > free enzyme 21082 20169 > ligand1 21073 20184 > ligand 2 21070 20151 > ligand3 20916 20150 > ligand 4 20901 20150 > please tell me does it show any fault in the simulation or how can i > interpret it? similarly there are slight diffrences in the total energy and > density of the system while all my ligands have similar structures > differing only in one or two atoms. > I have done all my work with your guidance as i have no other expert here > to guide me and now need little more guidance. can you suggest me some > literature regarding interpretation of such matters.Thanks in advance. > Regards > Neelam Wafa > Ph. D scholar > University of the Punjab Lahore, Pakistan > -- > 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 [email protected]. > -- 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 [email protected].
