[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug
ABEL Stephane
Stephane.ABEL at cea.fr
Mon Nov 5 19:19:10 CET 2018
Hello again,
Does the GROMACS team have some suggestions to help me to resolve my problem with the output of gmx densmap and xpm2ps to an eps/pdf with all the ticks in the x/y axis (see below)? Since it seems a small bug should I fiil a redmine?
Thanks
Stéphane
------------------------------
Message: 2
Date: Sun, 4 Nov 2018 13:19:06 +0000
From: ABEL Stephane <Stephane.ABEL at cea.fr>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from
gmx densmap [update] and possible bug
Message-ID:
<3E39B768BB199548AB18F7289E7534AF4887A9C5 at EXDAG0-B0.intra.cea.fr>
Content-Type: text/plain; charset="utf-8"
Hi again,
additional info about my issue with DensMap and xpm2ps
I noticed that the number of decimals of the x/y axis values ??in the xpm are smaller may have an effect of presence of the minor and major ticks in eps file obtained from xpm2ps (see below) Indeed with the same following params in the m2p
x-major = 1.00000
x-minor = 0.10000
x-firstmajor = 0.0
y-major = 1.00000
y-minor = 0.10000
y-firstmajor = 0.0
and different examples
1) With PDB as input and 1 frame I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are present in the eps
/* x-axis: 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1 1.05 1.1 1.15 1.2 1.25 1.3 1.35 1.4 1.45 1.5 1.55 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2 2.05 2.1 2.15 2.2 2.25 2.3 2.35 2.4 2.45 2.5 2.55 2.6 2.65 2.7 2.75 2.8 2.85 2.9 2.95 3 3.05 3.1 3.15 3.2 3.25 3.3 3.35 3.4 3.45 3.5 3.55 3.6 3.65 3.7 3.75 3.8 3.85 3.9 3.95 */
2) With PDB as input and 1000 frame I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are NOT present in the eps
/* x-axis: 0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 1.74957 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.59911 3.64909 3.69908 3.74907 3.79906 3.84904 3.89903 3.94902 */
3) With XTC as input and 1 frame I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are NOT present in the eps
/* x-axis: 0 0.0500004 0.100001 0.150001 0.200001 0.250002 0.300002 0.350003 0.400003 0.450003 0.500004 0.550004 0.600004 0.650005 0.700005 0.750005 0.800006 0.850006 0.900007 0.950007 1.00001 1.05001 1.10001 1.15001 1.20001 1.25001 1.30001 1.35001 1.40001 1.45001 1.50001 1.55001 1.60001 1.65001 1.70001 1.75001 1.80001 1.85001 1.90001 1.95001 2.00001 2.05002 2.10002 2.15002 2.20002 2.25002 2.30002 2.35002 2.40002 2.45002 2.50002 2.55002 2.60002 2.65002 2.70002 2.75002 2.80002 2.85002 2.90002 2.95002 3.00002 3.05002 3.10002 3.15002 3.20002 3.25002 3.30002 3.35002 3.40002 3.45003 3.50003 3.55003 3.60003 3.65003 3.70003 3.75003 3.80003 3.85003 3.90003 3.95003 */
and 4) With XTC as input and 1000 frames I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are NOT present in the eps
/* x-axis: 0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 1.74956 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.5991 3.64909 3.69908 3.74907 3.79906 3.84904 3.89903 3.94902 */
I used for the above examples the same densmap and xpm2ps commands show below and the 5.1.4 and 2018.2 gromacs version. It is a bug related to the rounding in the xpm2ps or I miss something ?
Thank you in advance for your help
St?phane
------------------------------
Message: 4
Date: Sat, 3 Nov 2018 17:45:53 +0000
From: ABEL Stephane <Stephane.ABEL at cea.fr>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from
gmx densmap
Message-ID:
<3E39B768BB199548AB18F7289E7534AF4887A94D at EXDAG0-B0.intra.cea.fr>
Content-Type: text/plain; charset="iso-8859-2"
Thanks you Justin for your help but I still have the smae problem . I have changed in my m2p file the floowing fields
x-major = 1.0 ; Major ticks on x axis every .. frames
x-minor = 0.05 ; Id. Minor ticks
x-firstmajor = 0.0 ; First frame for major tick
y-major = 1.0 ; Major ticks on y axis every .. frames
y-minor = 0.05 ; Id. Minor ticks
y-firstmajor = 0.0
and use the xpm, some (not all) sticks appeared in each axis but w/o the labels. I still do not understand why ...
St?phane
------------------------------
On 11/3/18 12:19 PM, ABEL Stephane wrote:
> Hello,
>
> I am using the below .m2p file as input for xpm2ps obtained from gmx densmap (v2018.2), but I am not able to get axis range label. The commands I use for densmap and xpm2ps
>
> gmx_mpi densmap -f MYXTC.xtc -s MYTPR.tpr -n MYINDEX.ndx -b 150000 -e 210000 -bin 0.5 -aver z -unit nm-2 -o MYXPM.xpm
>
> gmx_mpi xpm2ps -f MYXPM.xpm -di MYM2P.m2p -rainbow blue -gradient 0 0 0 -o MYEPS.eps
>
> The range in the xpm for the x and y axis are 0 to 12.5097 (see below)
>
> ---- m2p -----
>
> black&white = no
> linewidth = 1
> titlefont = Helvetica
> titlefontsize = 20
> legend = yes
> legendfont = Helvetica
> legendlabel =
> legend2label =
> legendfontsize = 14
> xbox = 0
> ybox = 0
> matrixspacing = 20
> xoffset = 0
> yoffset = 0
> boxlinewidth = 1
> ticklinewidth = 1
> zerolinewidth = 1
> x-lineat0value = none
> x-major = 15.0
Here's your problem. You're telling xpm2ps to place major tick marks
every 15 units, but:
> /* x-axis: 0 0.0500388 0.100078 0.150116 0.200155 0.250194 0.300233 0.350271 0.40031 0.450349 0.500388 0.550426 0.600465 0.650504 0.700543 0.750581 0.80062 0.850659 0.900698 0.950736 1.00078 1.05081 1.10085 1.15089 1.20093 1.25097 1.30101 1.35105 1.40109 1.45112 1.50116 1.5512 1.60124 1.65128 1.70132 1.75136 1.8014 1.85143 1.90147 1.95151 2.00155 2.05159 2.10163 2.15167 2.20171 2.25174 2.30178 2.35182 2.40186 2.4519 2.50194 2.55198 2.60202 2.65205 2.70209 2.75213 2.80217 2.85221 2.90225 2.95229 3.00233 3.05236 3.1024 3.15244 3.20248 3.25252 3.30256 3.3526 3.40264 3.45267 3.50271 3.55275 3.60279 3.65283 3.70287 3.75291 3.80295 3.85298 3.90302 3.95306 */
> /* x-axis: 4.0031 4.05314 4.10318 4.15322 4.20326 4.25329 4.30333 4.35337 4.40341 4.45345 4.50349 4.55353 4.60357 4.6536 4.70364 4.75368 4.80372 4.85376 4.9038 4.95384 5.00388 5.05391 5.10395 5.15399 5.20403 5.25407 5.30411 5.35415 5.40419 5.45422 5.50426 5.5543 5.60434 5.65438 5.70442 5.75446 5.8045 5.85453 5.90457 5.95461 6.00465 6.05469 6.10473 6.15477 6.20481 6.25484 6.30488 6.35492 6.40496 6.455 6.50504 6.55508 6.60512 6.65515 6.70519 6.75523 6.80527 6.85531 6.90535 6.95539 7.00543 7.05546 7.1055 7.15554 7.20558 7.25562 7.30566 7.3557 7.40574 7.45577 7.50581 7.55585 7.60589 7.65593 7.70597 7.75601 7.80605 7.85608 7.90612 7.95616 */
> /* x-axis: 8.0062 8.05624 8.10628 8.15632 8.20636 8.25639 8.30643 8.35647 8.40651 8.45655 8.50659 8.55663 8.60667 8.6567 8.70674 8.75678 8.80682 8.85686 8.9069 8.95694 9.00698 9.05701 9.10705 9.15709 9.20713 9.25717 9.30721 9.35725 9.40729 9.45732 9.50736 9.5574 9.60744 9.65748 9.70752 9.75756 9.8076 9.85763 9.90767 9.95771 10.0078 10.0578 10.1078 10.1579 10.2079 10.2579 10.308 10.358 10.4081 10.4581 10.5081 10.5582 10.6082 10.6583 10.7083 10.7583 10.8084 10.8584 10.9084 10.9585 11.0085 11.0586 11.1086 11.1586 11.2087 11.2587 11.3088 11.3588 11.4088 11.4589 11.5089 11.559 11.609 11.659 11.7091 11.7591 11.8091 11.8592 11.9092 11.9593 */
> /* x-axis: 12.0093 12.0593 12.1094 12.1594 12.2095 12.2595 12.3095 12.3596 12.4096 12.4597 12.5097 */
...your axis only goes to 12.5, so you get no labeling of any sort.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
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Message: 3
Date: Sun, 4 Nov 2018 10:03:51 -0600
From: Ali Ahmed <aa5635737 at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] TOPOLOGY AND GRO FILE ATOMS NAME MISMATCH
Message-ID:
<CAFqrJrqS11KZakEFUSxQrAXJZ_2ugPuwGLMjX9w9xq9W8LyPzg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi
I believe gromacs uses atom names from topology if they are not matching.
Check atoms in PDB and compare them with topology then you will find what
is missing or the differences
Ali
On Sun, Nov 4, 2018 at 7:05 AM K. Subashini <subashinik at hotmail.com> wrote:
> Hi gromacs users,
>
> For an organic molecule, the topology file was built using opls
> forcefield was obtained.
>
> Using gmx insert command, the gro file containing 150 molecules of the
> same organic compound placed in a box was obtained.
>
> Now the topology and gro file have non-matching atom names.
>
>
> How to fix the error?
>
> Thanks,
> Subashini.K
>
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