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

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 equilib

[gmx-users] Trouble with restrained dihedrals

nd 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 * Ple

Re: [gmx-users] Fumbling in the dark with dihedral pulling

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:

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

[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:

[gmx-users] Calculate dihedrals

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

[gmx-users] Python API Documentation question

nd 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 l

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 Pe

[gmx-users] runtime error: pdb2gmx issues in Python API

caught {} 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 las

Re: [gmx-users] Ran into trouble installing Gromacs API

"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

[gmx-users] Ran into trouble installing Gromacs API

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 a