Re: [gmx-users] Restart energy minimization with step .pdb files
Ok, thank you for the clarification; I thought those files where generated no
matter what.
By the way, I am not trying to restart because the simulation crashed: it's
just that I am running on a cluster and the job exceded the prescibed time
limit. The minimimization itself seems to work fine (at least this is what I
can see from ener.edr).
Cheers,
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 27 February 2020 13:11
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Restart energy minimization with step .pdb files
On 2/27/20 4:37 AM, Michele Pellegrino wrote:
> Hi,
>
>
> I am trying to restart steepest descent using the .pdb files generated by
> mdrun. The name of these files has the following pattern:
>
> step#%_n*.pdb
>
> being # and * integers and % a character ('a', 'b' or 'c').
>
> I read the documentation, but I can't understand what those files represent.
>
> Could anyone give me some hint?
step*.pdb files are the coordinates in each spatial domain in an attempt
to help you debug what is going on. I have never been able to employ
them in any useful way. All they really indicate is that your mdrun
process is going to crash due to instability.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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Re: [gmx-users] Restart energy minimization with step .pdb files
I am sorry, but I don't fully understand your answer: do you mean step_XXX.pdb
files are generated when atoms are overlapping?
In any case I still do not get the meaning of the labels; what 'a', 'b' and 'c'
stand for?
Thank you for your quick response.
Cheers,
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Quyen V. Vu
Sent: 27 February 2020 11:22
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Restart energy minimization with step .pdb files
It usually happens when you have two or more atoms overlap.
step_XXX.pdb is the lowest energy state that steepest descend can give you
with your input file.
In my opinion, you should look into the log file of energy minimization
step, find out which atom is exerted the maximum force, visualize your
initial input and check is there any atom overlaps with that atom.
Best,
On Thu, Feb 27, 2020 at 10:37 AM Michele Pellegrino wrote:
> Hi,
>
>
> I am trying to restart steepest descent using the .pdb files generated by
> mdrun. The name of these files has the following pattern:
>
> step#%_n*.pdb
>
> being # and * integers and % a character ('a', 'b' or 'c').
>
> I read the documentation, but I can't understand what those files
> represent.
>
> Could anyone give me some hint?
>
>
> Cheers,
>
> Michele
>
>
> p.s. I am running GROMACS 2019.5
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Restart energy minimization with step .pdb files
Hi,
I am trying to restart steepest descent using the .pdb files generated by
mdrun. The name of these files has the following pattern:
step#%_n*.pdb
being # and * integers and % a character ('a', 'b' or 'c').
I read the documentation, but I can't understand what those files represent.
Could anyone give me some hint?
Cheers,
Michele
p.s. I am running GROMACS 2019.5
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Re: [gmx-users] generating Doxygen documentation
Paul, thank you very much! Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Paul Bauer Sent: 12 February 2020 21:02 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] generating Doxygen documentation The correct address is http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/doxygen/html-full/index.xhtml Need to fix a link somewhere then I think. /Paul On Wed, 12 Feb 2020, 20:46 Michele Pellegrino, wrote: > Moreover: the link to Jenkins does not work (section 7.8.1, "Building the > documentation"): > > > http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml > > Cheers, > Michele > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Michele > Pellegrino > Sent: 12 February 2020 20:39 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] generating Doxygen documentation > > Mark, > > no such directory is produced after make (evein if the output is 'Built > target doxygen-all'). > The only Doxyfile I can utilize to generate html/latex documentation is > 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'. > > It seems I need to run cmake somewhere, somehow, but it's not really clear > to me in which directory (and with which options(s)). > > Cheers, > Michele > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: 12 February 2020 17:34 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] generating Doxygen documentation > > Hi, > > When they succeed, the doxygen targets produce files like > > $builddir/docs/html/doxygen/html-*/index.xhtml > > which you can open in your browser. The doxygen for the released versions > is on the web however, so it's much easier to just use or refer to that. > > Mark > > On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > > > Hi, > > > > > > I am trying to generate the Doxygen documentation for GROMACS from the > > files in /docs/doxygen. > > > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > > succesfully; I don't know what to do next: I tried to run cmake in the > > doxygen directory to generate the Doxyfiles, but I get the following > errors: > > > > """ > > > > CMake Error at CMakeLists.txt:36 (include): > > include could not find load file: > > > > gmxCustomCommandUtilities > > > > > > CMake Error at CMakeLists.txt:37 (include): > > include could not find load file: > > > > gmxOptionUtilities > > > > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > > Unknown CMake command "gmx_dependent_option". > > > > """ > > > > What should I do? > > > > > > Thanks for your attention, > > > > Michele > > > > > > p.s. I am referring to the github master branch current version > > -- > > 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 > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Li
Re: [gmx-users] generating Doxygen documentation
Moreover: the link to Jenkins does not work (section 7.8.1, "Building the documentation"): http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: 12 February 2020 20:39 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] generating Doxygen documentation Mark, no such directory is produced after make (evein if the output is 'Built target doxygen-all'). The only Doxyfile I can utilize to generate html/latex documentation is 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'. It seems I need to run cmake somewhere, somehow, but it's not really clear to me in which directory (and with which options(s)). Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: 12 February 2020 17:34 To: Discussion list for GROMACS users Subject: Re: [gmx-users] generating Doxygen documentation Hi, When they succeed, the doxygen targets produce files like $builddir/docs/html/doxygen/html-*/index.xhtml which you can open in your browser. The doxygen for the released versions is on the web however, so it's much easier to just use or refer to that. Mark On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > Hi, > > > I am trying to generate the Doxygen documentation for GROMACS from the > files in /docs/doxygen. > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > succesfully; I don't know what to do next: I tried to run cmake in the > doxygen directory to generate the Doxyfiles, but I get the following errors: > > """ > > CMake Error at CMakeLists.txt:36 (include): > include could not find load file: > > gmxCustomCommandUtilities > > > CMake Error at CMakeLists.txt:37 (include): > include could not find load file: > > gmxOptionUtilities > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > Unknown CMake command "gmx_dependent_option". > > """ > > What should I do? > > > Thanks for your attention, > > Michele > > > p.s. I am referring to the github master branch current version > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] generating Doxygen documentation
Mark, no such directory is produced after make (evein if the output is 'Built target doxygen-all'). The only Doxyfile I can utilize to generate html/latex documentation is 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'. It seems I need to run cmake somewhere, somehow, but it's not really clear to me in which directory (and with which options(s)). Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: 12 February 2020 17:34 To: Discussion list for GROMACS users Subject: Re: [gmx-users] generating Doxygen documentation Hi, When they succeed, the doxygen targets produce files like $builddir/docs/html/doxygen/html-*/index.xhtml which you can open in your browser. The doxygen for the released versions is on the web however, so it's much easier to just use or refer to that. Mark On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > Hi, > > > I am trying to generate the Doxygen documentation for GROMACS from the > files in /docs/doxygen. > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > succesfully; I don't know what to do next: I tried to run cmake in the > doxygen directory to generate the Doxyfiles, but I get the following errors: > > """ > > CMake Error at CMakeLists.txt:36 (include): > include could not find load file: > > gmxCustomCommandUtilities > > > CMake Error at CMakeLists.txt:37 (include): > include could not find load file: > > gmxOptionUtilities > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > Unknown CMake command "gmx_dependent_option". > > """ > > What should I do? > > > Thanks for your attention, > > Michele > > > p.s. I am referring to the github master branch current version > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] generating Doxygen documentation
Hi, I am trying to generate the Doxygen documentation for GROMACS from the files in /docs/doxygen. I following 2020 manual, I run 'make doxygen-all' in the build directory, succesfully; I don't know what to do next: I tried to run cmake in the doxygen directory to generate the Doxyfiles, but I get the following errors: """ CMake Error at CMakeLists.txt:36 (include): include could not find load file: gmxCustomCommandUtilities CMake Error at CMakeLists.txt:37 (include): include could not find load file: gmxOptionUtilities CMake Error at CMakeLists.txt:53 (gmx_dependent_option): Unknown CMake command "gmx_dependent_option". """ What should I do? Thanks for your attention, Michele p.s. I am referring to the github master branch current version -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] adding an external body force
Justin, thank you very much for the clarification. I believe the documentation should report 'add', instead of 'impose' (otherwise it may be confusing). Regards, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: 06 February 2020 14:47 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] adding an external body force On 2/6/20 4:58 AM, Michele Pellegrino wrote: > Hi, > > > I was wondering how to apply an external forcing term to one group; looking > at the 2020 documentation I found: > > > " > > accelerate group > On each atom in an "accelerate group" an acceleration a_g is imposed. This is > equivalent to an external force. > > " > > > However I would argue it is not equivalent at all: the contibution of an > external body force would add an acceleration term, not impose it, right? > > To make a more concrete example, what if I want to simulate gravity by > setting 'accelerate' to some value? Would I obtain free-falling or would > gravity be added on top of the force field from atomic intercations? The use of acceleration groups simply adds an acceleration to the one that arises from the forces in the simulation and acts in the update step. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] adding an external body force
Hi, I was wondering how to apply an external forcing term to one group; looking at the 2020 documentation I found: " accelerate group On each atom in an "accelerate group" an acceleration a_g is imposed. This is equivalent to an external force. " However I would argue it is not equivalent at all: the contibution of an external body force would add an acceleration term, not impose it, right? To make a more concrete example, what if I want to simulate gravity by setting 'accelerate' to some value? Would I obtain free-falling or would gravity be added on top of the force field from atomic intercations? Thanks for your attention. Michele -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] COM removal note
Hi, I am running some MD simulation using position restraints and turning-off centre of mass removal (comm-mode = None in the .mdp file). However, GROMACS 2020 still tell me with a note that 'removing center of mass motion in the presence of position restraints might cause artifacts'. So, is this note triggered by the use of restraints alone (so everything is fine), or am I doing something wrong (i.e. comm-mode = None? is not the right option for disabling com motion removal)? If it's the former case I believe it would be more user-friendly not to show the note in case the simulation involves position restraints AND no com motion removal. Thanks. Regards, Michele -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Charmm to Gromacs itps
Hi, have you tried gmx pdb2gmx -f ? Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of atb files Sent: 27 January 2020 10:51 To: gromacs.org_gmx-users Subject: [gmx-users] Charmm to Gromacs itps Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD simulation stops without any error/warning message
Alessandra, no core file was generated: I 'only' have the trajectory, the checkpoint state, the .edr file and the md.log file; none of them report an error message whatsoever. The only thing that comes to my mind is a crash because of a failure of the SIMD (I have set AVX2_128 when building GROMACS), could it be? Thank you for the suggestion by the way. Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Alessandra Villa Sent: 23 January 2020 14:38 To: gmx-us...@gromacs.org; gromacs.org_gmx-users Subject: Re: [gmx-users] MD simulation stops without any error/warning message Hi, On Thu, Jan 23, 2020 at 2:04 PM Michele Pellegrino wrote: > Hi, > > > today I was running a MD simulation and it stopped without any > error/warning message. > > It just stopped: the md.log file reported everything till the last time > step, and no information on the nature of the termination can be found in > the standard output and the standard error. > > I tried to restart the simulation using the last checkpoint but I got the > error message: > > --- > Program: gmx mdrun, version 2019.4 > Source file: src/gromacs/fileio/checkpoint.cpp (line 2435) > > Fatal error: > Failed to lock: md.log. Already running simulation? > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > So, I double-checked if the simulation was still running in the background > (and exponentially slowed down, for some reason) or if I accidentally > stopped the process in background (without killing it, though): no trace of > the process to be found. > I run gmx energy with the default ener.edr file to see if it stopped > because of some unphysical values for the temperature or the total energy, > but everything seems to have stayed bounded. > It is actually the second time I find myself in this situation: is there > another way to what find out could have gone wrong? > > If a core file was generated , you could look at it Best regards Alessandra > > Thank you. > > > Cheers, > > Michele > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
You are welcome, Christian. I see that you reported my initial message in the issue: I have to say the initial mismatch I reported was due to the script I was using for reading the file, and not to the file format itself, while the actual value for the mismatch is reported in the answer to David van der Spoel. Thanks. Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christian Blau Sent: 23 January 2020 13:30 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize Hi Michele, Thanks for the input and suggestion! I created a redmine issue using your observations that you can follow at https://redmine.gromacs.org/issues/3353 Best, Christian On 2020-01-23 11:03, Michele Pellegrino wrote: > Ok, I believe I have found the nature of this 'quirk' looking at the source > code (as Berk suggested me to do). > I was assuming a format, but GROMACS is producing another: the .dat file in > the output contains the values PLUS the coordinates for each bin, that is the > first row and the first colum are not denisty values, but coordinates; hence > the output matrix is indeed (n1+1)x(n2+1), the actual values being in > grid[1:n1-1,1:n2-1] (0-start index convention). > So apparently is not a bug in the code, but just a misunderstanding of me as > user; I double checked the documentation (both for 2019.04 and for the new > 2020 release) and I did not find any reference to the format of the output > file: could it be a good idea to incude some indication in that regard? > > Cheers, > Michele > > * there is a typo in the original message (2:n2-2 instead of 1:n2-1) > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: 22 January 2020 22:58 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap > doestnottmatchtprescribedtsize > > I tried just now: it did not work: 1728 values expected, 1645 values in the > .dat file. > I managed to make it work by defining the number of values in each direction > as (in Python): > Nx = np.sqrt(Nda*Lx/Lz) > Nz = Nx*Lz/Lx > Nx = int( np.round(Nx) ) > Nz = int( np.round(Nz) ) > being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght > of the simulation box in the x (z) direction (np stands for numpy). > However, I believe this manipulation should not be necessary. > > Cheers, > Michele > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of David van > der Spoel > Sent: 22 January 2020 22:07 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap > doestnottmatchtprescribedtsize > > Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino: >> Ok, thank you. >> I am counting the elements assuming they are in an array organized in a row >> major fashion. > have you tried supplying -n1 47 -n2 35 to be able to check manually? > > (by the way a resolution of 0.1 Angstrom is unlikely to give you a > smooth surface) >> Scarica Outlook per Android<https://aka.ms/ghei36> >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of Berk Hess >> >> Sent: Wednesday, January 22, 2020 6:34:47 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] .dat file from gmx densmap does not match >> prescribed size >> >> A grid element >> >> I looked at the code and it directly uses n1 and n2 you provide. So I >> thought that it might be that the code reading the file has a limit on the >> number of characters on a line. >> >> /Berk >> >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of Michele >> Pellegrino >> Sent: Wednesday, January 22, 2020 5:07 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] .dat file from gmx densmap does not match >> prescribed size >> >> >> What do you mean by 'element'? >> >> Anyway, part of the issue was in how I was reading the file; with a little >> modification of the script I reduced the mismatch, but it still persists. >> Could it be because GROMACS forces a grid with same meshwith in x and (in my >> case) z direction, so that the used should impose either -n1 OR -n2 (but not >> both)? Or maybe the issue is just in the format of the .dat output file? >> >> By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nano
[gmx-users] MD simulation stops without any error/warning message
Hi, today I was running a MD simulation and it stopped without any error/warning message. It just stopped: the md.log file reported everything till the last time step, and no information on the nature of the termination can be found in the standard output and the standard error. I tried to restart the simulation using the last checkpoint but I got the error message: --- Program: gmx mdrun, version 2019.4 Source file: src/gromacs/fileio/checkpoint.cpp (line 2435) Fatal error: Failed to lock: md.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- So, I double-checked if the simulation was still running in the background (and exponentially slowed down, for some reason) or if I accidentally stopped the process in background (without killing it, though): no trace of the process to be found. I run gmx energy with the default ener.edr file to see if it stopped because of some unphysical values for the temperature or the total energy, but everything seems to have stayed bounded. It is actually the second time I find myself in this situation: is there another way to what find out could have gone wrong? Thank you. Cheers, Michele -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
Ok, I believe I have found the nature of this 'quirk' looking at the source code (as Berk suggested me to do). I was assuming a format, but GROMACS is producing another: the .dat file in the output contains the values PLUS the coordinates for each bin, that is the first row and the first colum are not denisty values, but coordinates; hence the output matrix is indeed (n1+1)x(n2+1), the actual values being in grid[1:n1-1,1:n2-1] (0-start index convention). So apparently is not a bug in the code, but just a misunderstanding of me as user; I double checked the documentation (both for 2019.04 and for the new 2020 release) and I did not find any reference to the format of the output file: could it be a good idea to incude some indication in that regard? Cheers, Michele * there is a typo in the original message (2:n2-2 instead of 1:n2-1) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: 22 January 2020 22:58 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file. I managed to make it work by defining the number of values in each direction as (in Python): Nx = np.sqrt(Nda*Lx/Lz) Nz = Nx*Lz/Lx Nx = int( np.round(Nx) ) Nz = int( np.round(Nz) ) being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy). However, I believe this manipulation should not be necessary. Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: 22 January 2020 22:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino: > Ok, thank you. > I am counting the elements assuming they are in an array organized in a row > major fashion. have you tried supplying -n1 47 -n2 35 to be able to check manually? (by the way a resolution of 0.1 Angstrom is unlikely to give you a smooth surface) > > Scarica Outlook per Android<https://aka.ms/ghei36> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: Wednesday, January 22, 2020 6:34:47 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > A grid element > > I looked at the code and it directly uses n1 and n2 you provide. So I thought > that it might be that the code reading the file has a limit on the number of > characters on a line. > > /Berk > > ________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Wednesday, January 22, 2020 5:07 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > > What do you mean by 'element'? > > Anyway, part of the issue was in how I was reading the file; with a little > modification of the script I reduced the mismatch, but it still persists. > Could it be because GROMACS forces a grid with same meshwith in x and (in my > case) z direction, so that the used should impose either -n1 OR -n2 (but not > both)? Or maybe the issue is just in the format of the .dat output file? > > By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers > (if that may help understanding the issue). > > Thanks, > Michele > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: 22 January 2020 16:49 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match > prescribed size > > How are you counting the elements? Lines with 3531 elements are very long, so > they can easily exceed some limit. > > /Berk > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Tuesday, January 21, 2020 5:16 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size > > Hello, > > > I am struggling a little bit with gmx densmap. I am trying to obtain a matrix > with density values from the .dat file generated by the program; however the > number of data in the output file does not match what I am expecting. > > I tried to prescribe both the number of bins in each direction (-n1 and -n2 > options) and the grid size (-bin
Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
Ok, I believe I have found the nature of this 'quirk' looking at the source code (as Berk suggested me to do). I was assuming a format, but GROMACS is producing another: the .dat file in the output contains the values PLUS the coordinates for each bin, that is the first row and the first colum are not denisty values, but coordinates; hence the output matrix is indeed (n1+1)x(n2+1), the actual values being in grid[1:n1-1,2:n2-2] (0-start index convention). So apparently is not a bug in the code, but just a misunderstanding of me as user; I double checked the documentation (both for 2019.04 and for the new 2020 release) and I did not find any reference to the format of the output file: could it be a good idea to incude some indication in that regard? Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: 22 January 2020 22:58 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file. I managed to make it work by defining the number of values in each direction as (in Python): Nx = np.sqrt(Nda*Lx/Lz) Nz = Nx*Lz/Lx Nx = int( np.round(Nx) ) Nz = int( np.round(Nz) ) being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy). However, I believe this manipulation should not be necessary. Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: 22 January 2020 22:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino: > Ok, thank you. > I am counting the elements assuming they are in an array organized in a row > major fashion. have you tried supplying -n1 47 -n2 35 to be able to check manually? (by the way a resolution of 0.1 Angstrom is unlikely to give you a smooth surface) > > Scarica Outlook per Android<https://aka.ms/ghei36> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: Wednesday, January 22, 2020 6:34:47 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > A grid element > > I looked at the code and it directly uses n1 and n2 you provide. So I thought > that it might be that the code reading the file has a limit on the number of > characters on a line. > > /Berk > > ________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Wednesday, January 22, 2020 5:07 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > > What do you mean by 'element'? > > Anyway, part of the issue was in how I was reading the file; with a little > modification of the script I reduced the mismatch, but it still persists. > Could it be because GROMACS forces a grid with same meshwith in x and (in my > case) z direction, so that the used should impose either -n1 OR -n2 (but not > both)? Or maybe the issue is just in the format of the .dat output file? > > By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers > (if that may help understanding the issue). > > Thanks, > Michele > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: 22 January 2020 16:49 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match > prescribed size > > How are you counting the elements? Lines with 3531 elements are very long, so > they can easily exceed some limit. > > /Berk > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Tuesday, January 21, 2020 5:16 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size > > Hello, > > > I am struggling a little bit with gmx densmap. I am trying to obtain a matrix > with density values from the .dat file generated by the program; however the > number of data in the output file does not match what I am expecting. > > I tried to prescribe both the number of bins in each direction (-n1 and -n2 > options) and the grid size (-bin option), not at the same, of course: > > > gmx densmap -f
Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file. I managed to make it work by defining the number of values in each direction as (in Python): Nx = np.sqrt(Nda*Lx/Lz) Nz = Nx*Lz/Lx Nx = int( np.round(Nx) ) Nz = int( np.round(Nz) ) being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy). However, I believe this manipulation should not be necessary. Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: 22 January 2020 22:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino: > Ok, thank you. > I am counting the elements assuming they are in an array organized in a row > major fashion. have you tried supplying -n1 47 -n2 35 to be able to check manually? (by the way a resolution of 0.1 Angstrom is unlikely to give you a smooth surface) > > Scarica Outlook per Android<https://aka.ms/ghei36> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: Wednesday, January 22, 2020 6:34:47 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > A grid element > > I looked at the code and it directly uses n1 and n2 you provide. So I thought > that it might be that the code reading the file has a limit on the number of > characters on a line. > > /Berk > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Wednesday, January 22, 2020 5:07 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > > What do you mean by 'element'? > > Anyway, part of the issue was in how I was reading the file; with a little > modification of the script I reduced the mismatch, but it still persists. > Could it be because GROMACS forces a grid with same meshwith in x and (in my > case) z direction, so that the used should impose either -n1 OR -n2 (but not > both)? Or maybe the issue is just in the format of the .dat output file? > > By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers > (if that may help understanding the issue). > > Thanks, > Michele > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: 22 January 2020 16:49 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match > prescribed size > > How are you counting the elements? Lines with 3531 elements are very long, so > they can easily exceed some limit. > > /Berk > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Tuesday, January 21, 2020 5:16 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size > > Hello, > > > I am struggling a little bit with gmx densmap. I am trying to obtain a matrix > with density values from the .dat file generated by the program; however the > number of data in the output file does not match what I am expecting. > > I tried to prescribe both the number of bins in each direction (-n1 and -n2 > options) and the grid size (-bin option), not at the same, of course: > > > gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 > -aver y -n1 4772 -n2 3531 > > > OR (equivalently): > > > gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 > -aver y -bin 0.01 > > > In both cases I get a dimension mismatch (I expect 16849932 values but I get > 4359553). > > I am using GROMACS 2019.4?. > > > What am I doing wrong? > > > Thanks for your help. > > > Cheers, > > Michele > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List bef
Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
I will try, thank you for the tip. To be fair, this issue came up also when trying to set a meshwidth larger than the one GROMACS prescribes by default (I was trying 0.05 nm instead of 0.02 nm). Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: 22 January 2020 22:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino: > Ok, thank you. > I am counting the elements assuming they are in an array organized in a row > major fashion. have you tried supplying -n1 47 -n2 35 to be able to check manually? (by the way a resolution of 0.1 Angstrom is unlikely to give you a smooth surface) > > Scarica Outlook per Android<https://aka.ms/ghei36> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: Wednesday, January 22, 2020 6:34:47 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > A grid element > > I looked at the code and it directly uses n1 and n2 you provide. So I thought > that it might be that the code reading the file has a limit on the number of > characters on a line. > > /Berk > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Wednesday, January 22, 2020 5:07 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed > size > > > What do you mean by 'element'? > > Anyway, part of the issue was in how I was reading the file; with a little > modification of the script I reduced the mismatch, but it still persists. > Could it be because GROMACS forces a grid with same meshwith in x and (in my > case) z direction, so that the used should impose either -n1 OR -n2 (but not > both)? Or maybe the issue is just in the format of the .dat output file? > > By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers > (if that may help understanding the issue). > > Thanks, > Michele > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Berk Hess > > Sent: 22 January 2020 16:49 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] .dat file from gmx densmap does not match > prescribed size > > How are you counting the elements? Lines with 3531 elements are very long, so > they can easily exceed some limit. > > /Berk > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Michele > Pellegrino > Sent: Tuesday, January 21, 2020 5:16 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size > > Hello, > > > I am struggling a little bit with gmx densmap. I am trying to obtain a matrix > with density values from the .dat file generated by the program; however the > number of data in the output file does not match what I am expecting. > > I tried to prescribe both the number of bins in each direction (-n1 and -n2 > options) and the grid size (-bin option), not at the same, of course: > > > gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 > -aver y -n1 4772 -n2 3531 > > > OR (equivalently): > > > gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 > -aver y -bin 0.01 > > > In both cases I get a dimension mismatch (I expect 16849932 values but I get > 4359553). > > I am using GROMACS 2019.4?. > > > What am I doing wrong? > > > Thanks for your help. > > > Cheers, > > Michele > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Us
Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
Ok, thank you. I am counting the elements assuming they are in an array organized in a row major fashion. Scarica Outlook per Android<https://aka.ms/ghei36> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: Wednesday, January 22, 2020 6:34:47 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size A grid element I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line. /Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: Wednesday, January 22, 2020 5:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size What do you mean by 'element'? Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists. Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file? By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers (if that may help understanding the issue). Thanks, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: 22 January 2020 16:49 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit. /Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: Tuesday, January 21, 2020 5:16 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size Hello, I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting. I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course: gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531 OR (equivalently): gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01 In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553). I am using GROMACS 2019.4?. What am I doing wrong? Thanks for your help. Cheers, Michele -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] .dat file from gmx densmap does not match prescribed size
What do you mean by 'element'? Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists. Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file? By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers (if that may help understanding the issue). Thanks, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: 22 January 2020 16:49 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit. /Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: Tuesday, January 21, 2020 5:16 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size Hello, I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting. I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course: gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531 OR (equivalently): gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01 In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553). I am using GROMACS 2019.4?. What am I doing wrong? Thanks for your help. Cheers, Michele -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] .dat file from gmx densmap does not match prescribed size
Hello, I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting. I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course: gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531 OR (equivalently): gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01 In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553). I am using GROMACS 2019.4?. What am I doing wrong? Thanks for your help. Cheers, Michele -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
