[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

[Alan]

Thanks Ilja,

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
> 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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