[gmx-users] in vacu simulation

[Juliette N.]

On 15 February 2012 21:00, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> 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...
>

Thanks Justin and Mark. I think you meant 7.3.9 which I did when you
referred me to that. My problem was that I did not expect rc=0  is *just
defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent
to no interaction than infinite cutff off (all interactions). And also I
dont see why do we need to change rc to infinite. I mean if force fields
dictate cutoffs based on a distance where nonbonded interactions are close
enough to zero (negligible), what  purpose use of infinite cutoff serve?

>
>
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