VMD-L Mailing List

From: satya kumar (mail2mvskumar_at_gmail.com)
Date: Tue Jul 24 2012 - 10:11:19 CDT

According to the Gromacs fixed format, reducing the number of digits after
the decimal point will not effect the number of digits before the decimal.
If by chance the positions change, then this effects the decimal period
position. This is because of the decimal period has to be aligned.

Thanks,
Satya.

On Tue, Jul 24, 2012 at 10:09 AM, Jim Kress <jimkress_58_at_kressworks.org>wrote:

> 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. ****
>
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> *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.****
>
> ****
>
> ** **
>
> 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****
>
> ** **
>