[gmx-users] How to examine our created topology

[Faezeh Pousaneh]

Dear Justin

I have had asked you a question recently ''[gmx-users] How to examine our
created topology
<https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg09758.html>''.
and you helped me with giving ABT structure of the molecule I am studding,
lutiidne.

 late reply, but I was checking the given topology in ATB. I am afraid it
does not produce expected behavior in water solution. One for example; it
is known that they mix at room temperature, but the given structure demix.
That is the problem I also have in my own created topology. It is difficult
for me to get agreement with experiment for bulk lutidine, and its aqueous
solution at the same time.

Following this point, I would like to ask a general question ;
In order to study a binary mixture, for example lutidine and water here,
should I choose the charge distribution of lutidine (which I get from
quantum chemistry) from lutidine surrounded by lutidine, or lutidine
surrounded by water? that makes difference result in properties of bulk
lutidne and water lutidine mixture.

Best,
Best regards