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
double precision. Monitor the total energy and you will see it
drifting early on if you e.g. have a timestep that is too long. You
could also try to apply the constraints more accurately than default.
* Patriksson, A., Marklund, E., and Van der Spoel, D. (2007) Protein
Structures under Electrospray Conditions. Biochemistry, 56(4):933pp
* Marklund, E. G., Larsson, S. D., Patriksson, A., Van der Spoel, D.,
and Caleman, C. (2009) Structural stability of electrosprayed
proteins: temperature and hydration effects. Physical Chemistry
Chemical Physics, 11(36):8069pp
Modesto Orozco and coworkers have also simulated biomolecules in the
gas phase. I suggest to also have a look at their work.
Best,
On Mar 13, 2013, at 8:22 PM, Justin Lemkul wrote:
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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