VMD-L Mailing List

From: Jim Kress (jimkress_58_at_kressworks.org)
Date: Tue Jul 24 2012 - 09:09:37 CDT

Why do you not reduce the number of figures after the decimal point? Do you
really need this many significant figures? Then you could meet the
formatting requirements.

 

James Kress Ph.D., President

The KressWorks Foundation C

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

"Improving Lives One Atom At A Time" TM

(248) 605-8770

 

Learn More and Donate At:

 <http://www.kressworks.org> http://www.kressworks.org

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
satya kumar
Sent: Tuesday, July 24, 2012 8:21 AM
To: Bogdan Costescu
Cc: Axel Kohlmeyer; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Problem with Reading GROMACS file in VMD

 

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.

  <https://mail.google.com/mail/images/cleardot.gif>

 

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