VMD-L Mailing List

From: satya kumar (mail2mvskumar_at_gmail.com)
Date: Tue Jul 24 2012 - 07:21:24 CDT

Hello,

Here is an example taken from .gro file to make things clear:

2171OHX OW 5231 -0.543 -2.5801000.000
2171OHX HW1 5232 -0.510 -2.5471000.110

There is no white space between Y and Z coordinates, due to which Z
coordinate is read as 000.000, 000.110 and multiplied by a factor of 10 to
convert them to A.

Going by the Gro file format: "position (in nm, x y z in 3 columns, each 8
positions with 3 decimal places)". The example that I showed you before
follows the format. I still don't understand where exactly format is
violated.

I have used my own C++ ode to convert a data file to .gro file, and for my
project I do need large coordinates.

Thanks,

Satya.

On Tue, Jul 24, 2012 at 8:11 AM, Bogdan Costescu <bcostescu_at_gmail.com>wrote:

> On Tue, Jul 24, 2012 at 1:49 PM, satya kumar <mail2mvskumar_at_gmail.com>
> wrote:
> > I used fixed GROMACS fixed file format. In the coordinate columns, if you
> > have more than 4 digits before the decimal point, then you get into
> issue.
>
> Indeed, because that breaks the file format ;) So, don't expect any
> reader (be it the VMD reader plugin or GROMACS utilities) to be able
> to deal with it. How did you create this file ? An own script/utility
> ? And why do you need such large coordinates ?
>
> Cheers,
> Bogdan
>