<div dir="ltr">Hi Gavin,<br><br>A question arose for me: why did you consider the (rate = 0)?<br><br>Dariush<br> <br><br><div class="gmail_quote">On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh <span dir="ltr"><<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Justin<br>
<br>
Just a quick clarification regarding my previous point. With geometry =<br>
distance, and pull_dim =Y Y Y . Is the pull_group sampling all<br>
dimensions equally (or without prejudice) about pull_init ? And iN your<br>
first reply what did you mean about by "straight pull" ?<br>
<br>
Cheers<br>
<br>
Gavin<br>
<br>
Justin A. Lemkul wrote:<br>
><br>
><br>
> Gavin Melaugh wrote:<br>
>> Hi Justin<br>
>><br>
>> Thanks for the reply. I wanted my "pulling" to be free in all<br>
>> directions, that is in the liquid state with no defined reaction<br>
>> coordinate i.e not along a specific axis. This is why I used geometry =<br>
>> distance. Would you agree with this approach?<br>
><br>
> I suppose there is an argument that can be made for a more free<br>
> approach such as this one, but you're going to get the artifact you<br>
> observed the instant your pull group moves past a zero COM distance.<br>
> Whether or not this is a significant problem is something you'll have<br>
> to determine.<br>
><br>
> -Justin<br>
><br>
>> By free I mean. The absolute distance between the COG of the ref group<br>
>> and that of the pull group.<br>
>><br>
>> Cheers<br>
>><br>
>> Gavin<br>
>><br>
>> Justin A. Lemkul wrote:<br>
>>><br>
>>> Gavin Melaugh wrote:<br>
>>>> Dear all<br>
>>>><br>
>>>> I have a query regarding umbrella sampling simulations that I have<br>
>>>> carried out to study a dynamical process of a guest inserting into a<br>
>>>> host. I always get get a wall tending off to infinity at or just<br>
>>>> before<br>
>>>> the zero distance between the<br>
>>>> two species.<br>
>>>> The process I describe, for one system in particular, happens readily<br>
>>>> and I have compared the PMF from a non constrained simulation (via the<br>
>>>> RDF and reversible work theorem) and the same PMF from a set of<br>
>>>> umbrella sampling<br>
>>>> simulations. They agree quite well but in the non constrained<br>
>>>> simulation<br>
>>>> I get a minimum practically at zero whereas for the umbrella sampling<br>
>>>> the minimum is shifted and there is an infinite wall close to zero.<br>
>>>> This<br>
>>>> wall is not present from the reversible work theorem. Why the infinite<br>
>>>> wall? Why does the black histogram not centre around zero. Is this an<br>
>>>> artefact of the umbrella technique? Please see attached the profile<br>
>>>> from<br>
>>>> the umbrella sampling technique, and the corresponding histograms.<br>
>>>><br>
>>> What's happening is the COM reference distance is changing signs, so<br>
>>> you get an artifact. The "distance" geometry is relatively inflexible<br>
>>> and is only suitable for straight pulls of continuously increasing or<br>
>>> continuously decreasing COM distance. You should try using the<br>
>>> "position" geometry instead. There are some notes that you may find<br>
>>> useful in my tutorial:<br>
>>><br>
>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html</a><br>
>>><br>
>>><br>
>>><br>
>>> -Justin<br>
>>><br>
>>>> Here is an excerpt from one of the umbrella mdp files.<br>
>>>><br>
>>>> pull = umbrella<br>
>>>> pull_geometry = distance<br>
>>>> pull_dim = Y Y Y<br>
>>>> pull_start = no<br>
>>>> pull_ngroups = 1<br>
>>>> pull_group0 = cage_1<br>
>>>> pull_group1 = tail<br>
>>>> pull_init1 = 0<br>
>>>> pull_rate1 = 0.0<br>
>>>> pull_k1 = 10000<br>
>>>> pull_nstxout = 150<br>
>>>> pull_nstfout = 150<br>
>>>><br>
>>>><br>
>>>> Cheers<br>
>>>><br>
>>>> Gavin<br>
>>>><br>
>>>><br>
>>>> ------------------------------------------------------------------------<br>
>>>><br>
>>>><br>
>>>><br>
>>>> ------------------------------------------------------------------------<br>
>>>><br>
>>>><br>
>><br>
>><br>
><br>
<span class="HOEnZb"><font color="#888888"><br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><div>Kind Regards,<br>Dariush Mohammadyani<br>Department of Structural
Biology<br>University of Pittsburgh School of Medicine<br>Biomedical Science
Tower 3<br>3501 Fifth Avenue<br>Pittsburgh, PA 15261<br>USA</div></div><br>
</div>