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 Co
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
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:
Dear gmx users,
Recently I've been trying to install GROMACS 20201. After successfully
compilng GROMACS 2020.1, when executing make check command, I
encountered the following error. Specifically, one out of 56 tests failed,
which was related to Mdrun Test.WritesHelp. Looking at the error message,
I
On 4/5/20 7:13 AM, Quyen V. Vu wrote:
Dear Justin,
In your tutorial, you selected the initial configuration for each umbrella
by the radial distance between chain A and B [ r = sqrt(x^2+y^2+z^2)]
and in umbrella sampling simulation, your setting is:
pull_coord1_dim = N N Y
pull_coord1_start
Dear Justin,
In your tutorial, you selected the initial configuration for each umbrella
by the radial distance between chain A and B [ r = sqrt(x^2+y^2+z^2)]
and in umbrella sampling simulation, your setting is:
pull_coord1_dim = N N Y
pull_coord1_start = yes
so as the draw I attached here
