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

[neelam wafa]

Thanks sir Mark
It means the results are not faulty and I can continue for further work.
 Thanks for your valuable suggestions.
Regards

On Sat, 20 Apr 2019, 11:37 pm Mark Abraham, <mark.j.abraham at gmail.com>
wrote:

> 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, <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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