[gmx-users] CO2 virtual site

[Mark Abraham]

Hi,

On Fri., 20 Dec. 2019, 09:59 Sina Omrani, <sinaomrani96 at gmail.com> wrote:

> Hi,
> I have a problem when I use CO2 model with virtual sites during energy
> minimization. I used itp file in the md tutorial and beside the fact that
> some of my water molecules can not be settled, I get a positive potential
> energy and high force on molecules. Is something wrong?
>

Probably. How does it work without the CO2. Probably you just have clashing
atoms from your preparation process and need to fix that first.

And another question, Why virtual sites are introduced as atoms in itp file?
> [ atomtypes ]
> ; name  bond_type    mass    charge   ptype          sigma      epsilon
>   MCO   MCO          0.000   0.000    A              0.000      0.000
> You can see that it is "A" as an atom not "D" or "V".
>

Multi-atom linear molecules like CO2 are numerically awkward. So they are
typically modeled as linear diatomic and the positions and forces
interpolated between the diatomic and multi-atomic forms. Probably the docs
for your model talk about this, and you should read up on it.

Mark

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