[gmx-users] in vacu simulation

[Justin A. Lemkul]

Juliette N. wrote:
> Hi all,
> 
> I am trying to run simulation in vaccum using the the changes shown 
> below to the usual mdp file.
> pbc              =  no
> 
> ;coulombtype         =  PME   
> ;vdw-type            =  Shift   
> 
> ;        Cut-offs
> rlist               =  0   
> rcoulomb     =  0
> rvdw              =  0           
> 
> 
> nstlist             =  0               
> ns_type          =  simple
> 
> Can anyone help me with some short questions please?
> 
> 1- for pbc=no, I need to comment
> 
> ;coulombtype         =  PME   
> ;vdw-type            =  Shift  
> 
> so it defaults to vdw-type =  Cut-off which are not suitable algorithms. 
> Is using cut offs justified for in vacu runs?
> 

Plain truncations in condensed-phase systems lead to artifacts.  Neither of 
those conditions apply here, as you're using infinite cutoffs.

> 
> 2- I am not clear about using infinite cutoffs. Why one refers to 
> infinite cutoffs when
> 
> rlist               =  0   
> rcoulomb     =  0
> rvdw              =  0     ?
> 
> My understanding is that this settings means zero cutoff i.e no 
> interaction is calculated. Why does this setting refer to infinite rc?
> 
> 

That's the way the code works.  There are various parameters that can be set to 
-1, for instance, and that doesn't mean quantities are calculated every -1 steps ;)

Setting cutoffs to zero in this manner mean *all* interactions are calculated, 
not none.  Prove it to yourself with a zero-step MD run.  The nonbonded energy 
terms will not be zero, as they would in the case that no interactions would be 
calculated.

-Justin

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

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

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