[gmx-users] How to compare two pdb files

delara aghaie d_aghaie at yahoo.com
Sat Jun 16 15:06:57 CEST 2012

Dear Justin
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?


 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, 17:28
Subject: Re: [gmx-users] How to compare two pdb files

On 6/16/12 8:54 AM, delara aghaie wrote:
> Dear Justin
> I expected the gmxcheck program to print all the differences between nvt.tpr and
> npt.tpr.
> It seems that this only writes the velocities of atoms in x,y and z direction.
> Am I right?

No.  It prints all differences it finds.  Thus, if it's only printing velocities, all other information in the .tpr files is the same, but the velocities are different.


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

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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