[gmx-users] Implicit solvation: nonpolar term?

[Robert Darkins]

On 19/12/13 23:31, Justin Lemkul wrote:
>
>
> On 12/19/13 6:14 PM, rdwducl wrote:
>> Thanks for the reply Justin but I'm confused. Why must the atoms be 
>> bonded?
>>
>> Ultimately I plan to model micellisation whereby surfactants, which only
>> interact with each other via non-bonded terms, are driven to 
>> aggregate by
>> this nonpolar term...
>>
>
> I'm making a somewhat educated guess based on what you're observing.  
> A trivially simple test is to run two calculations with two particles 
> in a box - one in which a bond is defined between them, and one in 
> which there is no bond, but the atoms are at the same distance.  If 
> the results are different, my suspicion is confirmed (that the 
> topology controls whether or not two atoms impact one another's 
> surface accessibility).
>
> Give that a try and see what happens.
>
> -Justin
>

You appear to be correct.

In the md.log file /without/ any bonds:

  Computing:                               M-Number         M-Flops % Flops
-----------------------------------------------------------------------------
  NB VdW [V&F]                             0.003682 0.004    49.2
  NS-Pairs                                 0.000056 0.001    15.7
  CG-CoM                                   0.000014 0.000     0.6
  Virial                                   0.000104 0.002    25.0
  Stop-CM                                  0.000014 0.000     1.9
  Calc-Ekin                                0.000021 0.001     7.6
-----------------------------------------------------------------------------
  Total                                                       0.007 100.0
-----------------------------------------------------------------------------

whereas when a bond is added:

  Computing:                               M-Number         M-Flops % Flops
-----------------------------------------------------------------------------
  Born radii (HCT/OBC)                     0.000244 0.045    96.5
  Born force chain rule                    0.000024 0.000     0.8
  NS-Pairs                                 0.000001 0.000     0.0
  CG-CoM                                   0.000002 0.000     0.0
  Virial                                   0.000047 0.001     1.8
  Stop-CM                                  0.000004 0.000     0.1
  Calc-Ekin                                0.000004 0.000     0.2
  Lincs                                    0.000003 0.000     0.4
  Constraint-V                             0.000004 0.000     0.1
  Constraint-Vir                           0.000001 0.000     0.1
-----------------------------------------------------------------------------
  Total                                                       0.046 100.0
-----------------------------------------------------------------------------

So an atom will only 'see' another atom in computing the nonpolar term 
if it is bonded to it? That doesn't make sense in my mind. What am I 
missing?

Much appreciated.