[gmx-users] in vacu simulation

[Mark Abraham]

On 16/02/2012 12:22 PM, Justin A. Lemkul wrote:
>
>
> 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.
>

Or read about pbc=no in manual section 3.4.9 like I suggested Juliette 
do earlier this week...

Mark