[gmx-users] RDF(PMF) and Umbrella sampling

[Gavin Melaugh]

Hi Justin

Just a quick clarification regarding my previous point. With geometry =
distance, and pull_dim =Y Y Y . Is the pull_group sampling all
dimensions equally (or without prejudice) about pull_init ?  And iN your
first reply what did you mean about by "straight pull" ?

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Thanks for the reply. I wanted my "pulling" to be free in all
>> directions, that is in the liquid state with no defined reaction
>> coordinate i.e not along a specific axis. This is why I used geometry =
>> distance. Would you agree with this approach?
>
> I suppose there is an argument that can be made for a more free
> approach such as this one, but you're going to get the artifact you
> observed the instant your pull group moves past a zero COM distance. 
> Whether or not this is a significant problem is something you'll have
> to determine.
>
> -Justin
>
>> By free I mean. The absolute distance between the COG of the ref group
>> and that of the pull group.
>>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
>>>> Dear all
>>>>
>>>> I have a query regarding umbrella sampling simulations that I have
>>>> carried out to study a dynamical process of a guest inserting into a
>>>> host. I always get get a wall tending off to infinity at or just
>>>> before
>>>> the zero distance between the
>>>> two species.
>>>> The process I describe, for one system in particular, happens readily
>>>> and I have compared the PMF from a non constrained simulation (via the
>>>> RDF and reversible work theorem) and the same PMF from a set of
>>>> umbrella sampling
>>>> simulations. They agree quite well but in the non constrained
>>>> simulation
>>>> I get a minimum practically at zero whereas for the umbrella sampling
>>>> the minimum is shifted and there is an infinite wall close to zero.
>>>> This
>>>> wall is not present from the reversible work theorem. Why the infinite
>>>> wall? Why does the black histogram not centre around zero. Is this an
>>>> artefact of the umbrella technique? Please see attached the profile
>>>> from
>>>> the umbrella sampling technique, and the corresponding histograms.
>>>>
>>> What's happening is the COM reference distance is changing signs, so
>>> you get an artifact.  The "distance" geometry is relatively inflexible
>>> and is only suitable for straight pulls of continuously increasing or
>>> continuously decreasing COM distance.  You should try using the
>>> "position" geometry instead.  There are some notes that you may find
>>> useful in my tutorial:
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html
>>>
>>>
>>>
>>> -Justin
>>>
>>>> Here is an excerpt from one of the umbrella mdp files.
>>>>
>>>> pull        = umbrella
>>>> pull_geometry = distance
>>>> pull_dim = Y Y Y
>>>> pull_start = no
>>>> pull_ngroups = 1
>>>> pull_group0 = cage_1
>>>> pull_group1 = tail
>>>> pull_init1 = 0
>>>> pull_rate1 = 0.0
>>>> pull_k1 = 10000
>>>> pull_nstxout = 150
>>>> pull_nstfout = 150
>>>>
>>>>
>>>> Cheers
>>>>
>>>> Gavin
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>
>>
>