Thanks Ilja, On Tue, Jul 27, 2010 at 16:36, <[email protected]> wrote:
> I think the bond terms differ simply due to the round off error. The gro > file is worse than pdb when it comes to round off in Cartesian coordinates. > You can confirm this is the case by taking your gro file and converting it > back to pdb using gromacs tools and then use the resulting pdb (with the > same round of as the gro file now) file from gromacs in NAMD. You should > see > the same numbers for bonded terms then. > I doubt that would do any difference. Anyway, I tested with double precision and found out that my gro file is still rounded off like in single precision, i.e., my gro in double is the same in single and I was not expecting that. Example: pdb: 13 N ALA A 2 1.927 1.789 1.165 1.00 0.00 gro (single or double): 2ALA N 13 0.193 0.179 0.117 I was expecting gro when using pdb2gmx_d to be like: gro (single or double): 2ALA N 13 0.192700 0.178900 0.165000 Hummm.... I don't like this. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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