[gmx-users] Re: distance/direction PMF

[Gavin Melaugh]

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 ?

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Many thanks for the reply I know technically I am doing two different
>> things. However due to my starting conifgurations in both cases I would
>> expect similar results.
>> Could you confirm the following points
>>
>> 1) In pull_geometry=distance, and pull_dim =YYY; is the absolute
>> distance between the COM of both groups in all directions considered ?
>>
>
> Yes.
>
>> 2) In pull_geometry = direction, with a specified vector; I assume that
>> it is the distance between the two groups along this vector that is
>> considered?
>>
>
> Should be.  Compare the output of g_dist with what grompp reports as
> the initial distance.
>
>> 3) Is the specified vector taken to be the vector connecting the two
>> points? Therefore are the desired distances in the mdp files essentially
>> the magnitudes of this vector at each window.
>>
>
> Per the documentation, grompp normalizes the vector, so no, not
> directly.  But if you have proper settings for pull_init/pull_start,
> then the reference distance should be correctly calculated along the
> specified vector for each window.
>
> -Justin
>