Gavin Melaugh wrote:
Hi Justin
Thanks very much. One last question. What do you mean when you say "COM
reference distance is changing signs"? I thought the COM distance was
the absolute distance between the two groups and therefore cannot be
negative?
The pull code deals in vectors. Signs can change. The use of "distance" as a
geometry is perhaps somewhat misleading.
-Justin
Cheers
Gavin
Dariush Mohammadyani wrote:
Hi Gavin,
A question arose for me: why did you consider the (rate = 0)?
Dariush
On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh <gmelaug...@qub.ac.uk
<mailto:gmelaug...@qub.ac.uk>> wrote:
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
>>>>
>>>>
>>>>
------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
------------------------------------------------------------------------
>>>>
>>>>
>>
>>
>
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
