[gmx-users] Re: distance/direction PMF

[Gavin Melaugh]

Hi Justin

Sorry maybe I was unclear before with my first point; the specified
distance in the mdp file is 0.78nm, which grompp returns back as the ref
distance. The "distance at the start" that grompp returns is also
0.78nm, even though the actual distance is 0.815nm. That's why I was
asking what this distance actually means, as it is not the absolute
distance between the reference groups.
Also as regards to your second point; what if in the initial
configurations the two reference groups do not lie along the stated vector?

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> I did a short test on a particular window with the specified vector with
>> pull_init =0.78nm. I then grompp(ed) the final configuration and it gave
>> me a distance of 0.78 as the initial ditsance, fair enough. However when
>> I viewed the final line from g_dist the absolute distance or modulus was
>> 0.815 nm, which agreed with the distance I calculated using a molecular
>> configuration editor. My question is therefore this, when using
>> pull_geometry =direction with a specified vector, How should one
>> interpret the initial distance provided by grompp? and how does Gromacs
>> deal with the fact that the vector between the two point changes during
>> the run ?
>>
>
> You're telling grompp that the initial distance is 0.78 nm, so it's
> spitting that back out.  If that's not the true distance, then specify
> the correct quantity :)  The distance should be correctly detected with:
>
> pull_start = yes
> pull_init = 0
>
> As for the second question, the vector doesn't change over the
> simulation, but the position of pull_group1 along that vector will. 
> That's what the umbrella potential is doing - it allows for harmonic
> oscillation along any of the dimensions specified by pull_vec/pull_dim
> (depending on the settings).
>
> -Justin
>