[gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

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
>>
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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