From: RonitS Chem (ronits.chem95_at_gmail.com)
Date: Thu Aug 22 2019 - 21:15:18 CDT
I am pretty new to NAMD, and MD in general so please forgive me if this
question seems too naive/simplistic, but I have searched on this mailing
list a lot and cannot seem to find any solution for the question I have.
So, while learning how to run NAMD, I simulated just a water box and
calculated the RDF via VMD and the first solvation shell was fine but I had
a hard time getting the second solvation shell. I attributed this problem
to the rigid bonds, but still not sure since it is advised that for
2fs/step rigid bonds should be on.
Now, I am trying to simulate a single hydroxide ion in a water box using
the parameters given in the toppar_water_ion.str file. The RDF was
calculated between hydroxide oxygen and water oxygen, and it shows there
are 9 atoms in the first solvation shell, which does not seem correct.
I tried testing for ion O and water H, but that also shows 9 in the first
solvation shell with a distinct second shell, which is even weirder. After
looking through the literature, the RDF is definitely messed up, but the
reasoning is unclear.
I should mention that after parametrizing OH radical and running the same
input file but with a radical, in place of the ion, the RDFs match at least
one paper that I have been able to find.
Should I play with the values of timestep, rigidbonds or is the problem
Thank you for taking the time to read and any input will be appreciated.
This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:49 CST