Hi Mailtrack,
A direct way is to delete the loop information about H1 and H2 in water in the ZAFF.prep file. In this way there will be normal SHAKE on the O-H bonds in the metal coordinated waters.
The HOH angle force constant in TIP3P water in the AMBER force field is strong enough (about twice of that got by the Seminario method based on B3LYP/6-31G** level of theory), so I think deleting the H-H bonds would be fine for the metal coordinated waters.
Hope it helps,
Pengfei
> On Jun 17, 2019, at 12:10 PM, Hosein Geraili Daronkola <geraili.hsn.gmail.com> wrote:
>
> Dear all,
>
> I am using "ZAFF" for my system, and in the "center ID 6", there is a
> "LOOP" command in the "ZAFF.prep" which creates a bond between the two
> hydrogen of the water ("WT1") attached to the "ZN6". Because of this, I
> should use "noshakemask" for this "WT1" residue, but my question is, how
> can I avoid using 1 fs timestep because of this noshakemask, and also do I
> need to change "jfastw" for this change? "jfastw" uses 'WAT' as residue
> name to find the waters, and this residue is called "WT1", but the atom
> names (O, H1, H2) are the same.
> Or if I should use 1 fs timestep, why should I use SHAKE on hydrogens?
> Best
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Received on Thu Jun 20 2019 - 14:00:02 PDT
