[gmx-users] MD in Vacuum

[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  
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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