Re: [gmx-users] Installation on iPad
You can at least run SSH clients on iOS so you can technically edit text files and run commands from it even if the execution is not on the iPad. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 18 Apr 2020, at 14:43, Ali Khodayari mailto:ali.khoday...@student.kuleuven.be>> wrote: Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of course, considering the new iPad OS released. Kind regards, Ali -- 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<mailto: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] Trouble with restrained dihedrals
Bottom post: On 16 Apr 2020, at 08:56, Marko Petrovic mailto:ma...@kth.se>> wrote: Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for creating/updating the necessary files for several different simulation runs. The error message: ERROR 1 [file cv_restraints.itp, line 3]: Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. (after the function type). The .itp file contents: [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 5 7 915 1 1 -67.652 0 1 2 7 91517 1 159.806 0 1 2 Other possibly relevant file snippets: .mdp file define row (1st row): define= -DPOSRES_CV topol.top ifdef statement (last in file): #ifdef POSRES_CV #include "cv_restraints.itp" #endif I hope this is the info needed to easily see what I've done wrong. (Also info on how to interpret the error message would be nice, like which 5 parameters the software found and how it coun'ts parameters so I can get them to 3 or 6 if the problem is in the .utp file) With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology Also, the most up to date documentation on dihedral restraints I easily found was: http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints Is this still relevant? With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- 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] Trouble with restrained dihedrals
Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for creating/updating the necessary files for several different simulation runs. The error message: ERROR 1 [file cv_restraints.itp, line 3]: Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. (after the function type). The .itp file contents: [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 5 7 915 1 1 -67.652 0 1 2 7 91517 1 159.806 0 1 2 Other possibly relevant file snippets: .mdp file define row (1st row): define= -DPOSRES_CV topol.top ifdef statement (last in file): #ifdef POSRES_CV #include "cv_restraints.itp" #endif I hope this is the info needed to easily see what I've done wrong. (Also info on how to interpret the error message would be nice, like which 5 parameters the software found and how it coun'ts parameters so I can get them to 3 or 6 if the problem is in the .utp file) With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- 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] Fumbling in the dark with dihedral pulling
Thank you. I updated the mdp file. (Is the dihedral defined as a pair of planes rather than a triplet of vectors?) Unfortunately I still get the segmentation fault and similar warnings. I will try to compile the differences between the sample mdp and the one I used, then see which differences I can not understand and then just ask about those. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 6 Apr 2020, at 14:44, Justin Lemkul mailto:jalem...@vt.edu>> wrote: On 4/6/20 2:33 AM, Marko Petrovic wrote: I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin Your dihedral definitions are simply incorrect. pull_coord1_groups = 1 2 2 3 3 4 pull_coord2_groups = 2 3 3 4 4 5 should be pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -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<mailto: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.
Re: [gmx-users] Fumbling in the dark with dihedral pulling
I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 5 Apr 2020, at 23:09, Justin Lemkul mailto:jalem...@vt.edu>> wrote: On 4/5/20 5:05 PM, Marko Petrovic wrote: Hello. I've been trying to do coordinate pulling of dihedral angles of an alanine dipeptide in vacuum and used the umbrella sampling tutorial as a starting point. I'm trying to generate initial configurations for later runs, but the mdrun ends in a segmentation fault with error messages like: Step 15707, time 31.414 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025328, max 0.098100 (between atoms 11 and 13) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 90.40.1006 0.1054 0.0997 11 13 90.20.1110 0.1220 0. Step 15708, time 31.416 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 52572448.00, max 238546496.00 (between atoms 7 and 8) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 109.30.1054 23783084. 0.0997 9 11 119.50.1543 1995948.6250 0.1538 11 12 162.60.1127 1995948.6250 0. 11 13 115.60.1220 1995948.5000 0. 11 14 112.70.1124 1995948.6250 0. Wrote pdb files with previous and current coordinates Segmentation fault: 11 Perhaps the seg fault is not related to the warnings at all but as I am not certain what they mean and do think they are enough to cause some problems anyway I would like to understand them in general and also know what columns previous and current are saying. They refer to bond lengths, what the length was at the previous step and what it is now, compared to what the reference value should be. Your values indicate catastrophic distortion of the structure. As the original tutorial was done for a water solution and mine is conducted in vacuum I am guessing my modifications to the .mdp files are not completely updated so any tips on that woul also be helpful. There's no way to provide any useful advice without you posting your .mdp file. Note that the umbrella sampling tutorial has basically no relevance to anything you're doing because enforced dihedral rotation didn't exist when I wrote it :) -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<mailto:jalem...@vt.edu> | (540) 231-3129 http://www.thelemkullab.com<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<mailto: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] Fumbling in the dark with dihedral pulling
Hello. I've been trying to do coordinate pulling of dihedral angles of an alanine dipeptide in vacuum and used the umbrella sampling tutorial as a starting point. I'm trying to generate initial configurations for later runs, but the mdrun ends in a segmentation fault with error messages like: Step 15707, time 31.414 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025328, max 0.098100 (between atoms 11 and 13) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 90.40.1006 0.1054 0.0997 11 13 90.20.1110 0.1220 0. Step 15708, time 31.416 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 52572448.00, max 238546496.00 (between atoms 7 and 8) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 109.30.1054 23783084. 0.0997 9 11 119.50.1543 1995948.6250 0.1538 11 12 162.60.1127 1995948.6250 0. 11 13 115.60.1220 1995948.5000 0. 11 14 112.70.1124 1995948.6250 0. Wrote pdb files with previous and current coordinates Segmentation fault: 11 Perhaps the seg fault is not related to the warnings at all but as I am not certain what they mean and do think they are enough to cause some problems anyway I would like to understand them in general and also know what columns previous and current are saying. As the original tutorial was done for a water solution and mine is conducted in vacuum I am guessing my modifications to the .mdp files are not completely updated so any tips on that woul also be helpful. With RegardsMarko PetrovicEducatorComputational Science and TechnologySchool of Electrical Engineering and Computer ScienceKTH Royal Institute of Technology -- 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] Calculate dihedrals
Hello I want to calculate som singular dihedral values and I know this is simple, but can't figure out the usage of "gmx gangle" . I tried using "gmx angle" but the results were not what I was hoping for as it calculates an average of the specified angles and seems to be meant for averaging many angles calculations. Using the .gro and .ndx files from my call to "gmx angle" gmx angle -f start.gro -n test.ndx -type dihedral to a all to "gmx gangle" gmx gangle -g1 dihedral -f start.gro -n test.ndx this starts a dialogue where I initially tried selecting groups defined in the .ndx file, no error message suggests I've been successful. Pressing ctrl+d ends the run with the following message: > Reading frames from gro file 'GROningen Mixture of Alchemy and Childrens' Stories', 22 atoms. Last frame 0 time0.000 Analyzed 1 frames, last time 0.000 But I can't find any output anywhere. What am I missing? With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- 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] Python API Documentation question
Hello As I'm quite new to both gromacs in and of itself and the python API I'm struggling a bit figuring out how to go about getting simulations running using the API. I've managed to write a Python script creating and running shell command line commands to run through the Lysozyme tutorial, but that totally circumvents the API. The API has a function "commandline_operation" which I believe should also be usable for this, unfortunately I can't say I'm totally clear on the nomenclature used in the documentation so I'm unsure of what or where I go wrong. For example the executable parameter and arguments parameter in "gmx grompp"... is gmx the executable withh grompp a parameter or grompp the executable and the rest of the line parameters? And input_files and output_files, are they meant to be declared in those parameters only, in arguments only or both, and do flag keys need the dash prefix? I will be very thankful for any help anyone can give regarding this. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- 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] runtime error: pdb2gmx issues in Python API
I forgot to include my questions:
Questions:
- What is the cause python exception?
- Is there a more detailed documentation for gmx.commandline_operation() than
gmxapi basic
package<http://manual.gromacs.org/current/gmxapi/userguide/pythonreference.html#id1>
With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology
On 4 Feb 2020, at 15:53, Marko Petrovic mailto:ma...@kth.se>>
wrote:
Hello
I'm trying to create a python implementation using the API of the entire
lysozyme tutorial and have gotten stuck on the pdb2gmx step and can't decipher
the error message nor figure out if my thinking is fundamentally wrong for this
step. As can be seen in the code, I have tried to brute force my way to a
solution as well.
test=gmx.commandline_operation(executable = "pdb2gmx",
arguments = ["-water", "spce"
,"-ff", "oplsaa"
]
#,"-f",file_name
#,"-o",out_name)
,
#)
input_files = {"-f":file_name},
output_files = {"-o":out_name})
test.run()
this gives the following error message as a result of a compound exception:
raise exceptions.ApiError(message) from e
gmxapi.exceptions.ApiError: Uncaught {} while providing output-publishing
resources for {}.
Full error message included in attachment.
With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology
--
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] runtime error: pdb2gmx issues in Python API
Hello
I'm trying to create a python implementation using the API of the entire
lysozyme tutorial and have gotten stuck on the pdb2gmx step and can't decipher
the error message nor figure out if my thinking is fundamentally wrong for this
step. As can be seen in the code, I have tried to brute force my way to a
solution as well.
test=gmx.commandline_operation(executable = "pdb2gmx",
arguments = ["-water", "spce"
,"-ff", "oplsaa"
]
#,"-f",file_name
#,"-o",out_name)
,
#)
input_files = {"-f":file_name},
output_files = {"-o":out_name})
test.run()
this gives the following error message as a result of a compound exception:
raise exceptions.ApiError(message) from e
gmxapi.exceptions.ApiError: Uncaught {} while providing output-publishing
resources for {}.
Full error message included in attachment.
With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology
Traceback (most recent call last):
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 1799, in __publishing_context
yield resource
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 1979, in update_output
runner()
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 2574, in runner
operation_details(resources)
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 2752, in __call__
self._runner(resources)
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 2099, in __call__
self.function(**resources)
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/commandline.py",
line 151, in cli
stderr=subprocess.STDOUT,
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py",
line 395, in check_output
**kwargs).stdout
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py",
line 472, in run
with Popen(*popenargs, **kwargs) as process:
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py",
line 775, in __init__
restore_signals, start_new_session)
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py",
line 1436, in _execute_child
executable = os.fsencode(executable)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/os.py",
line 809, in fsencode
filename = fspath(filename) # Does type-checking of `filename`.
TypeError: expected str, bytes or os.PathLike object, not NoneType
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "P2_Lysozyme.py", line 92, in
main()
File "P2_Lysozyme.py", line 85, in main
test.run()
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 2236, in run
self.__resource_manager.update_output()
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 1952, in update_output
with self.local_input(i) as input:
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/contextlib.py",
line 112, in __enter__
return next(self.gen)
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 2021, in local_input
kwargs = self._input_edge.sink(node=member)
File "/Users/markopetrovic/Box
Sync/Egenstudier/AÌk5/P3/Ex-Jobb/StringMethodMaster/masters_venv/lib/python3.7/site-packages/gmxapi/operation.py",
line 1693, in sink
results[key] = self.resolve(key, node)
File "/Users/markopetrovic/Box
Sync/Egenstu
Re: [gmx-users] Ran into trouble installing Gromacs API
Thank you I'll try the other user guide and let you know as soon as I have made a new attempt. To help me understand documentation navigation issues better, can you tell me how you ended up at the readthedocs.io<http://readthedocs.io> site while installing GROMACS 2020? I followed the "Quick start" link from this page: https://gmxapi.readthedocs.io/en/latest/ And I hoped that it would be gmx2020 compatible. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 20 Jan 2020, at 11:27, Eric Irrgang mailto:ericirrg...@gmail.com>> wrote: Hi Marko, I'm sorry for the confusion. The install instructions for gmxapi 0.1 on GROMACS 2020 are at http://manual.gromacs.org/current/gmxapi/userguide/install.html I plan to update readthedocs in the next few days to cover both gmxapi 0.0.7 on GROMACS 2019 and gmxapi 0.1 ( https://github.com/kassonlab/gmxapi/issues/249), but I see that the reorganization of the repository leads to extra confusion (as you describe) so I will also update the old install docs. ( https://github.com/kassonlab/gmxapi/issues/252) To help me understand documentation navigation issues better, can you tell me how you ended up at the readthedocs.io site while installing GROMACS 2020? From: Marko Petrovic Subject: [gmx-users] Ran into trouble installing Gromacs API Hello I have (I think successfully) installed Gromacs 2020 on my computer (MacOS X Catalina) and tried to install the API using the quick install guide: https://gmxapi.readthedocs.io/en/latest/quickstart.html and get stuck on the step: pip install -r requirements.txt as that file does not seem to be in that folder of the repo. I found the file "requirements-test.txt" in the folder "python-packaging" and tried with that but got a long error message of missing stuff I didn't understand, I'm hoping those error messages are from the file not being intended for use inn the manner I tried so I'm currently not including those here. Should I have installed gromacs 2019 for which the API was developed? Has anyone else installed the API recently and (hopefully) exxperienced and overcome this hurdle? With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- 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] Ran into trouble installing Gromacs API
Hello I have (I think successfully) installed Gromacs 2020 on my computer (MacOS X Catalina) and tried to install the API using the quick install guide: https://gmxapi.readthedocs.io/en/latest/quickstart.html and get stuck on the step: pip install -r requirements.txt as that file does not seem to be in that folder of the repo. I found the file "requirements-test.txt" in the folder "python-packaging" and tried with that but got a long error message of missing stuff I didn't understand, I'm hoping those error messages are from the file not being intended for use inn the manner I tried so I'm currently not including those here. Should I have installed gromacs 2019 for which the API was developed? Has anyone else installed the API recently and (hopefully) exxperienced and overcome this hurdle? With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- 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.
