Yang Ye wrote:
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.'
you can use the SPC216 box without any modification. just change the
topology.
D. Egorov,
USMA, Russia, Yekaterinburg.
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________________________________________________________________________
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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