VMD-L Mailing List

From: satya kumar (mail2mvskumar_at_gmail.com)
Date: Sun Jul 22 2012 - 22:06:42 CDT

Hello All,

I am a VMD user, experiencing an issue with reading coordinates in VMD from
a Gromacs file. Sample coordinate from GRO file is:

1OHX OW 5231 -0.543 -2.5801000.000
1OHX HW1 5232 -0.510 -2.5471000.110

where the "position (in nm, x y z in 3 columns, each 8 positions with 3
decimal places)". {X,Y,Z} = {-0.543, -2.580, 1000.00} and {X,Y,Z} =
{-0.510, -2.547, 1000.110}. When we view in VMD, these numbers are
multiplied with a factor 10 to convert to Angstrom, then in particular Z
coordinates are converted to 000 and 0.110 respectively. In VMD the above
coordinates taken as:

{-5.429999828338623 -25.801000595092773 0.0}
{-5.099999904632568 -25.47100067138672 1.100000023841858}

These create problems with respect to analysis, in particular the Z
coordinate. Can someone guide me to fix this issue.

Thanks,
Satya.