[gmx-users] help with g_hydorder and g_polystat

[Emmanuel, Alaina]

No, using a trajectory file with g_hydorder hasn't made any difference. The error is still the same.

When I use g_polystat, I use the following command: 

g_polystat_d -f file.xtc  -s file.tpr -n polymer_backbone.ndx  -p persist.xvg -o polystat.xvg

Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, than using the whole polymer structure in an index file. 

Kind Regards,

Alaina

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 01 May 2013 10:58
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at 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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