[gmx-users] g_wham

[Gavin Melaugh]

Thanks Justin

Is it possible to use g_wham with pull_geometry = direction, I read on
the website that you couldn't but was wondering if this had changed?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi All
>>
>> I am using COM pulling to pull two molecules together in order to
>> calculate the potential of mean force and the pulling is fine. I am
>> using pull = umbrella for the pulling as I am following
>>  the tutorial on the website. If I use pull = constraint does this still
>> pull the molecules together, and if so do you still then need to
>> perform umbrella sampling on the configurations generated? I am a little
>> confused  as I don't understand how the molecules pull together if they
>> are constrained.
>>
>
> For plain SMD, you can use any of the pull methods.  In the tutorial I
> wrote, I explain why I used "pull = umbrella" during SMD.  Umbrella
> sampling is a separate procedure, which can be done after SMD.  If you
> want a free energy along the reaction coordinate, there are several
> methods for doing this, among which is umbrella sampling.
>
> -Justin
>
>> Many Thanks
>>
>> Gavin
>