[gmx-users] water tutorial
Yang Ye
leafyoung81-group at yahoo.com
Sat May 6 16:36:27 CEST 2006
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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