[gmx-users] water tutorial

[Yang Ye]

Hi, Egorov

You shall change it back to 1.86206.

As calculated from
Molecular weight of water: 15.9994+1.008*2=18.0154
Density = 216*18.0154*1.66054E-27(kg)/(1.86206^3 nm3) = 1000.843198 kg/m3

If the box size is altered as what is given by the pdb2gmx, the 
resulting water density will be 835kg/m3.

Why there is a change? A bug?

Yang Ye

Егоров Д.А. wrote:
> Dear Gromax list members,
>  
> I am trying to convert spc216.gro to tip3p216.gro. And to learn how to 
> do this I try water tutorial. But input spc216.gro included in the 
> tutorial has box dimentions 1.86206 in all three axes, but if I do 
> pdb2gmx -f spc216.pdb -o spc216.gro -p spc216.top then I obtain 
> spc216.gro with the next box dimentions 1.96800 1.99700 1.96900 at the 
> bottom of the .gro file. So is this difference important for 
> subsequent equilibration and if yes what can I do to obtain box sizes 
> given in tutorial spc216.gro.
>  
> D. Egorov,
> USMA, Russia, Yekaterinburg.
> ------------------------------------------------------------------------
>
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