[gmx-users] loss of precision in *.gro

[David van der Spoel]

On Wed, 2002-09-11 at 09:01, Mehmet Suezen wrote:
> Hello,
> 
> As far as you compiled gromacs in double precision, your trajectory 
> records are double.(for example in trr). Basicly your analysis tools
> (trajectory averages) worked without loss of precision. Anyway for 
> conventional classical molecular dynamics f8.3 starting structure is not
> that bad.(if one assume equilibrium structure will reached shortly)
> Do you think classical MD can predict better then 0.01 A?
> But if one goes to quantum mechanical regime, it may affect. 
> Or single structure analysis would absolutely affected as well. 
> As you said, cutting out from trr would be a solution in your case.
> I'd guess Idea of optimized geometry is to obtaine plausable starting 
> structure for QM input,As you said, cutting out from trr would be a
> solution 
> in this case.
Don't forget that the .g96 file format is also available. It has all the
precisionin  a float, which can be worthwhile in some cases.
Maybe we should make this the default instead of .gro? .pdb is not an
option because of lacking velocities.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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