[gmx-users] problem getting correct ramachandran plots

[Madhuri Agashe]

Hi,
I checked and found that I had not saved the trajectory in the first
10seconds, but had saved it every 20 seconds. 

g_rama -f 3_run2.trr -s 3_run2.tpr -o rama_first.xvg -b 1 -e 20

but even then, the command above did not give me the expected result ie
the plot for just the first 20 seconds.

Can you help?
-Madhuri

Madhuri Agashe
Graduate Research Assistant,
Dept. of Bioengineering,
Clemson University,
Clemson, SC 29631
Phone: 864-653-4230 (resi)
            864-656-1352 (off.)


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of David
Sent: Thursday, October 23, 2003 2:52 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] problem getting correct ramachandran plots

On Thu, 2003-10-23 at 00:23, Madhuri Agashe wrote:
> I am trying to get the Ramachandran plot for the first 10 ps and the
> last 10ps of a 600ps MD run.
> 
>  
> 
> The following command
> 
> g_rama -f 3_run2.trr -s 3_run2.tpr -o rama_last.xvg -b 590 -e 600
> 
> gave me the correct output for the last 10ps of the run.
> 
>  
> 
> But, when I tried 
> 
> g_rama -f 3_run2.trr -s 3_run2.tpr -o rama_first.xvg -b 1 -e 10
> 
> it did not get the data for only the first 10ps, but got the data for
> all 600ps!
> 
>  
> 
run gmxcheck -f 3_run2.trr
have you saved your trajectory at all during the first 10 ps?
Maybe you want to use the xtc file.


> Can anyone shed more light on why this might be happening?
> 
>  
> 
> Madhuri Agashe
> 
> Graduate Research Assistant,
> 
> Dept. of Bioengineering,
> 
> Clemson University,
> Clemson, SC 29631
> 
> Phone: 864-653-4230 (resi)
> 
>            864-656-1352 (off.)
> 
>  
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.