Fwd: [gmx-users] xpm2ps

[Justin Lemkul]

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.gandhiau at gmail.com>
> Date: 10 September 2013 18:35
> Subject: Re: [gmx-users] xpm2ps
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>
> I am attaching the files for your reference.
>
> On 10 September 2013 17:57, Justin Lemkul <jalemkul at 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
>>
>> jalemkul at 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
>
>

-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================