[gmx-users] query about different number of solvent molecules added

[neelam wafa]

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