[gmx-users] loss of precision in *.gro
David van der Spoel
spoel at xray.bmc.uu.se
Wed Sep 11 09:31:49 CEST 2002
On Wed, 2002-09-11 at 09:01, Mehmet Suezen wrote:
> 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
> 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.
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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