subject:"\[gmx\-users\] MD in Vacuum"

Re: [gmx-users] MD in Vacuum

2013-03-14 Thread Erik Marklund

Hi, You also need to consider the ensemble you want to investigate. If you simulate under constant energy you need a shorter timestep than you would have in solution and probably double precision. In the articles I list below we used a timestep of 0.5 fs and 1 fs, respectively, and

[gmx-users] MD in Vacuum

2013-03-13 Thread Lara Bunte

Hello In all my tutorials for md they investigate a molecule in solution. I want to do md simulations in vacuum and I did not find a good tutorial. So I want to ask you what should I do for a md simulation in vaccum? I take a molecule, optimize the structure, generate a topology with gromacs

Re: [gmx-users] MD in Vacuum

2013-03-13 Thread Justin Lemkul

On 3/13/13 12:53 PM, Lara Bunte wrote: Hello In all my tutorials for md they investigate a molecule in solution. I want to do md simulations in vacuum and I did not find a good tutorial. So I want to ask you what should I do for a md simulation in vaccum? Consult the literature.