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

neelam wafa neelam.wafa at gmail.com
Sat Apr 20 14:16:51 CEST 2019

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.
Neelam Wafa
Ph. D scholar
University of the Punjab Lahore, Pakistan

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