[gmx-users] Umbrella sampling and PMF calculations

[Alex]

So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this setup? I'd understand if the entire membrane was reactive, but it
isn't. Also, the obtained free energy value is very close to what one gets
by simply integrating the pullf data wrt pull coordinate, which makes
perfect sense. Any comments/suggestions?

Thanks,

Alex

On Fri, Jun 2, 2017 at 11:26 AM, Alex <nedomacho at gmail.com> wrote:

>
>
>>>
>> Yes, because if your ion diffuses laterally (or whatever constitutes your
>> "hole"), then you're not sampling what you think you're sampling.  That's
>> what the cylinder geometry is for.  You have a system capable of
>> significant lateral movement, so if you fail to apply a bias that acts in
>> the x-y plane, your results are very quickly going to become garbage.
>>
>> -Justin
>>
>> Of course. I actually realized that you used COM distance and not e.g.
> direction-periodic (which won't accept zero pulling rates anyway) only
> after I asked.
> Specifying somewhat awkward structures like disks as references could be
> avoided by simply allowing a component of the COM distance vector and not
> the entire vector) to be used. Anyway, doesn't really matter.
>
> Thanks,
>
> Alex
>