[gmx-users] Problem with accelerations

2017-05-24 Thread Kamps, M.
Mark, I'm not really sure what you mean by technique. I assume NEMD stands for Non-equilibrium MD? That is the case in my simulation.. About my simulation: I am trying to simulate a fluid flow between surfaces. Two atomistic surfaces of gold atoms have been created at Z=0 and Z=z, where z is the

Re: [gmx-users] Problem with accelerations

2017-05-23 Thread Kamps, M.
Mark, I'm not really sure what you mean by technique. I assume NEMD stands for Non-equilibrium MD? That is the case.. About my simulation: I am trying to simulate a fluid flow between surfaces. Two atomistic surfaces of gold atoms have been created at Z=0 and Z=z, where z is the top of the box.

Re: [gmx-users] Problem with accelerations

2017-05-23 Thread Mark Abraham
Hi, Which technique are you using for this? https://redmine.gromacs.org/issues/1354 speculates that this code is just broken, has been so for years, and should be removed given that nobody wishes to do the work to fix it ( :-( ) Mark On Tue, May 23, 2017 at 11:13 AM Kamps, M.

[gmx-users] Problem with accelerations

2017-05-23 Thread Kamps, M.
Dear GMX users, I have some strange behaviour which I cannot explain. I want to accelerate atoms through my box at a certain velocity. Since I can only adjust the acceleration, I have to trial-and-error my way to the right accelerations. To do this, I create a smaller 'testing' simulation,