[gmx-users] water tutorial

[David van der Spoel]

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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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