[gmx-users] Re: Umbrella Profile

[Steven Neumann]

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


>
> 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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