[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition
alanwilter at gmail.com
Tue Jul 27 18:06:13 CEST 2010
On Tue, Jul 27, 2010 at 16:36, <gmx-users-request at gromacs.org> 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
> 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.
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 Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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