[gmx-users] Re: Umbrella Profile

[Steven Neumann]

On Fri, May 18, 2012 at 1:27 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
> On Fri, May 18, 2012 at 12:22 PM, Justin A. Lemkul <jalemkul at vt.edu>wrote:
>
>>
>> I have no idea why you observe the dip, but it's probably irrelevant as
>> you don't need a reaction coordinate that long, if this is the same plot
>> that we've been discussing on the list.
>>
>> I must ask that you always post to the mailing list, for your own
>> benefit, especially in the immediate future as I will be traveling for some
>> time and will not reply very quickly to email; you stand a better chance
>> getting help from others.  I am also generally unable to dedicate much time
>> debugging others' research on a personal level.
>>
>> -Justin
>>
>> Thank you Justin. I decreased the reaction coordinate and this dip still
> occurs:
>
> http://speedy.sh/2qHNa/Profile2.JPG
>
> Its because of the applied weight of WHAM. Any suggestions please?
>
> Steven
>

Hi Justin,

I run umbrella sampling of my ligand binding to different part of my
residues. Each time my PMF profile is smooth but at the end the small dip
occurs. Here another example:

http://speedy.sh/dbUg9/ProfileHA1.JPG

http://speedy.sh/8zZ52/HistoHA1.JPG

What can be causing this? Shall I just igonore this taking the plateau
value or run a longer simulations in each window?

Best,

Steven



>
>
>>
>> On 5/18/12 4:17 AM, Steven Neumann wrote:
>>
>>> Dear Justin,
>>>
>>>
>>> I run umbrella sampling (pulling ligand away from the protein)
>>> simulations to
>>> get deltaG:
>>>
>>> http://speedy.sh/XpUks/**Profile.JPG<http://speedy.sh/XpUks/Profile.JPG>
>>>
>>> http://speedy.sh/yvJKx/**Histogram.JPG<http://speedy.sh/yvJKx/Histogram.JPG>
>>>
>>> I know I need one more window around 1 nm but apart from this histrogram
>>> looks
>>> really good. My each window was 50 ns.
>>>
>>> Why the plateau in the end goes down of 0.4 kcal/mol? Would you suggest
>>> longer
>>> simulation in each window?
>>>
>>> Thank you and sorry for writing straight to your email,
>>>
>>> Best
>>>
>>> Steven
>>>
>>>
>>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>>
>
>
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