[gmx-users] in vacu simulation

[Mark Abraham]

On 16/02/2012 3:14 PM, Juliette N. wrote:
>
>
> On 15 February 2012 23:05, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 16/02/2012 2:08 PM, Juliette N. wrote:
>>
>>
>>     On 15 February 2012 21:00, Mark Abraham <Mark.Abraham at anu.edu.au
>>     <mailto: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).
>
>     Sure, but reading the documentation is usually a better idea than
>     making assumptions :)
>
>     The underlying reason for this behaviour is that it is much easier
>     for the person writing the code to have one parameter that
>     occasionally has a "special" meaning when it takes a nonsense
>     value (like rc<=0) then it is to have a slew of parameters that
>     have to be managed when they are input (and checked, and
>     documented) and then possibly passed through a cascade of
>     functions (lots of bureaucracy and chances to make errors) before
>     they are used. The alternative costs the programmer more time. In
>     an ideal world there would be an infinite amount of such time, but
>     given the amount most people are prepared to pay for scientific
>     software, that time is severely limited.
>
>
>>     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?
>
>     Efficiency, like I said in the first post in this thread. Given
>     that your force field was parametrized with given cut-offs for the
>     condensed phase, to what purpose do you wish to calculate in
>     vacuo? The perturbation from calculating in vacuo will be much
>     larger than the perturbation from the use of infinite cut-offs.
>
>
>
> Thank you. I am looking at potential of a single molecule in vacu for 
> heat of vap purposes at different temperatures by changing ref_temp 
> and gen_temp for each run.

So it's much more bureaucracy every nstlist>0 steps to take your N atoms 
and look at their distance from the other N-1 atoms and make lists of 
which ones are inside rc than it is to just compute them all every step 
and know that if they're further than rc then the effect is tiny. For 
small enough N, the later is guaranteed to be faster...

Mark
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