On 9/10/13 6:43 AM, Neha Gandhi wrote:
Hi Justin,
I am sorry to forward the files to your id but gromacs mailing list
wouldn't allow attachments.
Regardless, please keep the discussion on the list. An .m2p file is small
enough that it can be copied and pasted into an email. Everything else should
be posted online such that you can provide a URL to download other files.
The image simply appears stretched, so the solution is to increase the ratio of
ybox/xbox, by decreasing xbox by a few orders of magnitude and/or increasing
ybox. Keep in mind that if you have a million frames and even a few hundred
residues along the y-axis, your x-axis is still 10^4 units larger! The current
ratio established by
xbox = 0.1 ; x-size of a matrix element
ybox = 5 ; y-size of a matrix element
is only 50, so you naturally see a very stretched and unintelligible plot.
-Justin
Many thanks,
Neha
---------- Forwarded message ----------
From: Neha Gandhi <n.gandh...@gmail.com>
Date: 10 September 2013 18:35
Subject: Re: [gmx-users] xpm2ps
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
I am attaching the files for your reference.
On 10 September 2013 17:57, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/10/13 5:30 AM, Neha Gandhi wrote:
Hi Gromacs mailing list supporters,
I had previously posted query on xpm2ps.
http://lists.gromacs.org/pipermail/gmx-users/2013-April/080729.html
There are 1000000 frames in the simulations. I tried fiddling with the
parameters in the .m2p file such as matrix spacing and X-axis minimum
and maximum tick spacing however I always get black lines at the
bottom instead of X-axis.
An image of what you're dealing with would be useful, as would the full
contents of the .m2p file you're using. Without that, there's not much
anyone can do to help, aside from generically saying to increase the value
of xtick.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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