[gmx-users] MD in Vacuum

[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.  Tutorials will not cover every topic, and since most MD 
force fields were designed for condensed-phase simulations, it's awfully hard to 
explain to a new user why we're making wild changes to "normal" settings and 
hope that they understand :)

> I take a molecule, optimize the structure, generate a topology with gromacs and what after this? Do I also have to make a box? what is the procedure?
>

Usually in vacuo simulations are done in the absence of periodicity and with 
infinite cutoffs.  In general, an approach like the following is used:

comm-mode = Angular
nstlist = 0
rlist = 0
rvdw = 0
rcoulomb = 0
pbc = no
ns-type = simple
vdwtype = cutoff
coulombtype = cutoff

Check literature to be sure to establish a protocol with some basis in precedent.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================