[gmx-users] problem getting correct ramachandran plots
magashe at CLEMSON.EDU
Mon Oct 27 19:22:00 CET 2003
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?
Graduate Research Assistant,
Dept. of Bioengineering,
Clemson, SC 29631
Phone: 864-653-4230 (resi)
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 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
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users