From: RonitS Chem (ronits.chem95_at_gmail.com)
Date: Thu Aug 22 2019 - 21:15:18 CDT
Hello everyone,
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
elsewhere?
Thank you for taking the time to read and any input will be appreciated.
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