[gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:
> 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.
> 

I have no idea why this is happening.  If you'd like me to troubleshoot further 
and see if I can get to the bottom of this, please send me (off-list is OK):

1. Coordinate file
2. Topology file(s)
3. The .mdp file that is giving the weird result

-Justin

> 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
>>>>
> 

-- 
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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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