Re: RDF of hydroxide ion in a water box

From: Haohao Fu (
Date: Mon Sep 02 2019 - 01:19:31 CDT

Hello Ronit,

You may want to have a look at a more recent water model. For example,
TIP3P-FB and TIP4P-FB in do well
in modeling a correct 1st/2nd/3rd hydration shell. OPC and OPC3 are also
excellent water models.


RonitS Chem <> 于2019年9月2日周一 上午3:12写道:

> Hello all,
> After reading through some literature, I came across that TIP3P water
> model does not show long range behavior properly. Besides TIP4P, TIP5P
> model is the only one which replicates the second and third solvation shell
> properly, as mentioned in this paper:
> , and its reference
> on TIP3P water and a modified model called TIP3P-Ewald.
> The only modification that the paper:
> suggested was in the LJ
> potential terms of Oxygen and Hydrogen. After making the same
> modifications, I see the second and third solvation shells in the rdf but
> there was a significant overbinding, and the density is messed up. Since
> the work I am doing strictly focusses on TIP3P water model, I am benching
> the idea of getting proper long range behavior, but I do want to understand
> more.
> I guess my question is why in some models, there are no Hydrogen LJ
> parameters, and how to make sense of changes in LJ parameters physically? I
> mean without running an actual simulation, how to predict what changes
> might occur in a system on tweaking the epsilon and Rmin/2 a little.
> Best,
> Ronit
> On Thu, Aug 22, 2019 at 7:17 PM RonitS Chem <>
> wrote:
>> 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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