[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug
ABEL Stephane
Stephane.ABEL at cea.fr
Wed Nov 7 16:26:34 CET 2018
Hello Justin,
It is not clear to me it is bug. but I "think" that in these particular case densmap does not truncate/rounds the data according to the bin value (i.e. 0.05) I used in gmx densmap command line. To correct this I wrote a short script that change the x-y values like where the x/y values are proportional to the bin value :
before :
/* x-axis: 0 0.0500004 .... 3.95003 */ ....
after
/* x-axis: 0 0.05 .... 3.95 */ ....
and then I can obtain the ticks with gmx xpm2ps and the m2p.
So by filling a redmine this problem will be reported and may be corrected
Stéphane
------------------------------
Message: 2
Date: Wed, 7 Nov 2018 10:06:05 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Regarding xpm2ps with a xpm file obtained
from gmx densmap [update] and possible bug
Message-ID: <b3846b6a-3da5-842d-290b-06a8a85202f4 at vt.edu>
Content-Type: text/plain; charset=iso-8859-2; format=flowed
On 11/5/18 1:19 PM, ABEL Stephane wrote:
> 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?
Is it actually a bug or do you just have extremely inconvenient data
that are difficult to assign convenient tick marks?
-Justin
> Thanks
>
> St?phane
>
>
>
> ------------------------------
>
> 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
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
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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
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>> send a mail to gmx-users-request at gromacs.org.
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
------------------------------
Message: 3
Date: Wed, 7 Nov 2018 16:06:45 +0100
From: Quyen Vu Van <vuqv.phys at gmail.com>
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Question about nsttcouple
Message-ID:
<CA+CKAfw9Qnj1gLjgban7dWVcV_9Y4E069_JZEha96adbrtN+nA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
nsttcouple=10 means that nsstcouple*dt(2fs, I guess)=0.02 and your
tau-t=0.1 (5 fold)
when nsttcouple=20, nsstcouple*dt=0.04 so your tau-t is only 2.5 fold. I
think so
On Wed, Nov 7, 2018 at 3:43 PM minky son <minky0710 at gmail.com> wrote:
> Dear gmx users,
>
>
> In gromacs manual,
>
> ?nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
> unless nstlist <=0, then a value of 10 is used.?
>
>
>
> When I did grompp with the following mdp options,
>
> nstlist = 20
>
> tcoupl = berendsen
>
> nsttcouple = -1
>
> tau-t = 0.1
>
>
>
> I got a warning message.
>
> WARNING 1 [file pr_nvt.mdp]:
>
> "For proper integration of the Berendsen thermostat, tau-t (0.1) should
> be at least 5 times larger than nsttcouple*dt (0.04)"
>
>
>
> I think this means that nsttcouple is applied to 20, not 10. This doesn't
> match with the one mentioned in the manual. why?
>
>
>
>
>
> When I also tried nstlist=10, grompp didn?t show any warning.
>
> But the value of nstlist was automatically changed to 40 in mdrun.
>
> Is nsttcouple applied to 10 in this case?
>
>
>
> Please give me an advice.
>
> Thank you.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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------------------------------
Message: 4
Date: Wed, 7 Nov 2018 16:06:45 +0100
From: Quyen Vu Van <vuqv.phys at gmail.com>
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Question about nsttcouple
Message-ID:
<CA+CKAfw9Qnj1gLjgban7dWVcV_9Y4E069_JZEha96adbrtN+nA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
nsttcouple=10 means that nsstcouple*dt(2fs, I guess)=0.02 and your
tau-t=0.1 (5 fold)
when nsttcouple=20, nsstcouple*dt=0.04 so your tau-t is only 2.5 fold. I
think so
On Wed, Nov 7, 2018 at 3:43 PM minky son <minky0710 at gmail.com> wrote:
> Dear gmx users,
>
>
> In gromacs manual,
>
> ?nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
> unless nstlist <=0, then a value of 10 is used.?
>
>
>
> When I did grompp with the following mdp options,
>
> nstlist = 20
>
> tcoupl = berendsen
>
> nsttcouple = -1
>
> tau-t = 0.1
>
>
>
> I got a warning message.
>
> WARNING 1 [file pr_nvt.mdp]:
>
> "For proper integration of the Berendsen thermostat, tau-t (0.1) should
> be at least 5 times larger than nsttcouple*dt (0.04)"
>
>
>
> I think this means that nsttcouple is applied to 20, not 10. This doesn't
> match with the one mentioned in the manual. why?
>
>
>
>
>
> When I also tried nstlist=10, grompp didn?t show any warning.
>
> But the value of nstlist was automatically changed to 40 in mdrun.
>
> Is nsttcouple applied to 10 in this case?
>
>
>
> Please give me an advice.
>
> Thank you.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-request at gromacs.org.
------------------------------
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