[gmx-users] How to compare two pdb files

delara aghaie d_aghaie at yahoo.com
Sat Jun 16 15:19:00 CEST 2012

Dear Justin

Thanks for your explanation, but the problem is when the results are printed out on screen, we can see only the end part of it, as the window does not let us to see the whole output. Is there any way to solve this?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: delara aghaie <d_aghaie at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 June 2012, 17:41
Subject: Re: [gmx-users] How to compare two pdb files

On 6/16/12 9:06 AM, delara aghaie wrote:
> Dear Justin
> Ok,
> I looked at gmxcheck help. There is an option to have output in latex format
>   -m        doc.tex  Output, Opt. LaTeX file
> so I used this command line:
> gmxcheck -s1 nvt.tpr -s2 npt.tpr -m doc.tex
>   again I could see result on the screen but the expected doc.tex file did not
> come out?

When supplying both -s1 and -s2 (or other combinations like -f and -f2), you're telling gmxcheck to compare files.  If you want a .tex file printed out, you need to analyze only one .tpr file.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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