[gmx-users] Re: Issue with GROMACS file format

Justin Lemkul jalemkul at vt.edu
Tue Jul 24 14:22:10 CEST 2012

On 7/24/12 8:18 AM, SatyaK wrote:
>   Thanks Justin for your reply.
>   Going by the Gromacs file format: "position (in nm, x y z in 3 columns,
> each 8 positions with 3 decimal places)"
>   It is not clear to me as to how many digits before the decimal point can a
> coordinate column accepts in the Gro file- Is it 3 or 4 digits before the
> decimal point? (If it is 3 digits before the decimal then there should be a
> white space between coordinate columns.)

Theoretically, the .gro format can accept 4 digits before the decimal point (8 
total columns, 3 used for after the decimal and one for the decimal point, which 
leaves 4).  The problem in your case is that VMD does not correctly parse the 
value even though it is technically acceptable within Gromacs.  One normally 
does not deal with coordinates on the order of 1000 nm, so whoever wrote the VMD 
plugin for changing coordinate file formats probably didn't account for that.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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