[gmx-users] Umberella sampling

[mohsen ramezanpour]

Thank you very much Dr.Justin for your important notes


On Wed, Apr 6, 2011 at 8:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>  I had asked this question before but unfortunately I didn't answered
>> good!
>>
>> Instead of Pulling and separating some structures in definite distances,
>> I located my drug in definite distances along z axis (as my initial
>> structures for doing umbrella sampling).
>> Am I right?
>>
>>
> I have no idea.  Presumably, if you've defined the reaction coordinate
> appropriately and distributed configurations along this vector at adequate
> intervals to sample the whole coordinate, then yes.
>
>
>  The main problem underlying this question is :
>>  Do we need to know the velocity of drug in every structure we choose for
>> doing umbrella sampling?(do they need to include the velocities too?)
>>
>
> PMF is calculated from either the resulting positions (in pullx.xvg) or
> forces (pullf.xvg) from the harmonically restrained simulations.
>
>
>  if no,which criteria assures with this K our molecule can cover the length
>> of it's windows?
>>
>>
> You can't necessarily know a priori if your force constants are adequate.
> Unfortunately, it's a bit empirical.  Run some simulations and analyze the
> result with g_wham.  A smooth PMF with good overlap between the histograms
> indicates your sampling is (at least) good, if not optimal on the first try.
>
>
>  Because I have chosen windows with different lingthes,And I want now to
>> choose K so that it can sweep the lengthes.
>>
>>
> Weaker force constants allow for more oscillation, but again, there is no
> prescribed way to know what values to choose.  If you have some very large
> window, you assign a weaker force constant, but then you may not cover the
> entire sampling window without a longer simulation in this window such that
> your molecule wanders through all of the applicable configuration space.
>
> -Justin
>
>
>  Thanks in advance for your reply
>>
>>
>>
>>
>>
> --
> ========================================
>
> 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
>
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