Re: [AMBER] output of diffusion data doesn't show two columns for big number values

From: Daniel Roe <>
Date: Sat, 19 Oct 2013 10:32:09 -0600


We need some more information in order to help. Which version of
AmberTools are you using, what was your exact input to ptraj, and
exactly which output file shows this issue? As far as I can see from
the code, this should never happen with the 'diffusion' command since
all output format specifiers have spaces in between them, e.g.:

fprintf(diffusionInfo->outputx, "%8.3f %8.3f",

Even if the numbers are larger than 8 characters there should still
always be a space between them. Does the same thing happen if you use


On Sat, Oct 19, 2013 at 5:01 AM, Vijay Manickam Achari
<> wrote:
> Dear Sir,
> I am calculating diffusion for water in a membrane system using ptraj.
> Since my simulation time is quite long (300ns), my diffusion value is big.
> I supposed to get something like below:
> 249985.00 13132.505
> but I get both values combined as:
> 249985.0013132.505.
> This gives no room for the two columns and xmgrace does not show graph when I try to plot.
> I also tried to use awk to separate those columns but it treat as only single column upon both columns combine together.
> Is there any tweaks need to do in ptraj for make the columns wider when writing their output?
> I need help.
> Thanks in advance.
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Oct 19 2013 - 10:00:02 PDT
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