On 4/30/13 9:00 PM, Emmanuel, Alaina wrote:
Hello Justin,
My mdp file shows that the pbc was set to xyz.
Instead of analyzing a coordinate file, does it work with a trajectory?
Regarding g_polystat and the nan's, what command are you issuing?
-Justin
Kind Regards,
Alaina
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat
On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
Dear All,
I'm fairly new to gromacs and having a bit of problem with the g_hydorder and
g_polystat. Thanks in advanced for your time.
For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm
Error:
Internal error in pbc_dx, set pbc has nor been called
For more information..
----------------------------------------
I'm not sure what this means. It seems to be implying that I don't have a box
around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x
4.94. Any ideas?
What is your setting for the pbc keyword in the .mdp file?
For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat
units smaller than 50 these usually show "nan" values, that cannot be plotted. From reading the gmx
threads I've found that Nan stands for "Not a Number", but why do these "nan" values
appear and how can I prevent it so that I can read in my results?
This could be an underlying problem related to the above interpretation of
periodicity. We don't have enough information to say for sure yet.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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