[gmx-users] Re: distance/direction PMF

[Gavin Melaugh]

Yeah

 I set pull_init =0, and pull_start = yes, and it still gave a "distance
at start" as 0.78nm. It must be doing something funny because with
pull_vec, because when I use pull_geometry = distance and pull_dim
= Y Y Y, the distance 0.815nm is returned as the "distance at start",
which is the actual distance between the two groups.

Cheers

Gavin
 
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> 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.
>
> As I said before, you're telling grompp to make that the reference
> distance. You say "the specified distance in the mdp file is 0.78 nm,"
> therefore grompp is doing what it's told.  If that's not the desired
> distance, then don't set it as such.  Have you tried the combination I
> suggested in the last message?  Does it give an initial distance of
> 0.815 nm?
>
>> Also as regards to your second point; what if in the initial
>> configurations the two reference groups do not lie along the stated
>> vector?
>>
>
> Hard to say, but probably you'll get some very high forces at the
> outset of the simulation as the simulation as the umbrella potential
> tries to force the pulled group to conform to the restraint
> specifications.  Whether or not that negatively impacts the ultimate
> result of the simulation is also an important consideration.  If
> you're pulling along a given vector, you should start with your
> reference coordinates as close to the desired location as possible.
>
> -Justin
>
>> 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
>>>
>>
>