Hi Priti,
Leena is correct that you grid parameters need to be adjusted. A grid spacing of dr=0.025 is recommended. You may want to consider increasing nr to 32768 or 65536 as dilute aqueous ionic solutions often require larger grids to capture long-range effects. A good practice is to look at %FLAG DELHV0 in the resulting Xvv file. You should find good numerical agreement between oppositely charged sites. For example,
%FLAG ATOM_NAME
%FORMAT(20A4)
O H1 Na+ Cl-
%FLAG DELHV0
%FORMAT(1P5E24.16)
-3.9777302600343534E-01 -3.9774346034206409E-01 -7.7002198757532101E+00 -7.6989475286399101E+00
Start with nr=16384 and increase if you don’t see numerical agreement as above.
The reason for these grid parameters is that 1D-RISM is 1D in the sense that only radial distance is consider. So nr*dr is the maximum separation between solvent sites. dr should be quite small to capture the detail of the solvation shells.
Also, the density of water at ambient conditions is about 1 g/cm^3. I would expect 1D-RISM to have trouble converging for a density of 2.85 g/cm^3 but it may work.
Hope this helps,
Tyler
> On May 17, 2018, at 6:23 AM, Leena Aggarwal <leena.hrc.gmail.com> wrote:
>
> This is for getting the xvv file of bulk solvent . This file will be used
> for 3D RISM calculations. While performing 3D RISM calculations you will
> define the box size according to the protein water system. In 1D RISM you
> can use nr=16384 and dr=0.025.
>
> On 17 May 2018 18:34, "PRITI ROY" <priitii.roy.gmail.com> wrote:
>
>> Hii Leena,
>>
>> Thank you for your response.
>>
>> The simulation box size of my protein water is 120x90x90, that's why I took
>> such large no. of grid points. Do I need to increase the steps?
>>
>> Best,
>> Priti
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Received on Thu May 17 2018 - 09:00:02 PDT
