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
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