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

Mark Abraham mark.j.abraham at gmail.com
Sat Apr 20 20:37:12 CEST 2019


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.


On Sat., 20 Apr. 2019, 14:17 neelam wafa, <neelam.wafa at gmail.com> 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
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