[gmx-users] Umbrella sampling

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Sorry I am not sure that I follow. Will the window with r0 =0.80 giving
> the distribution centred around 0.78nm not drive my free energy profile
> up. If I remove this window prior to running g_wham the free energy goes
> down. Should I increase the force constant so that the mean of the
> window is 0.80nm (bearing in mind that this is near the barrier region).
> 

If you have an incomplete or otherwise discontinuous free energy profile, then 
you won't get a correct result, but it's not simply due to "oversampling" one 
region.  It's that the "oversampling" results in "undersampling" another region. 
  Increasing the force constant for the window centered around 0.80 nm should work.

-Justin

> Gavin
> XAvier Periole wrote:
>> You can present the data differently:
>> you have two windows at 0.78 nm giving different distribution.
>>
>> That indicates these windows are not converged. Does not mean
>> that the others (0.80 nm) are converged :))
>>
>> On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote:
>>
>>> Hi Xavier
>>>
>>> Thanks for the reply. With respect to your answer of my first query.
>>> What if you had two windows practically on top of each other, but one
>>> was not supposed to be there. e.g A window with r0 of 0.80 nm and
>>> centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm.
>>>
>>> Gavin
>>>
>>> XAvier Periole wrote:
>>>> On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote:
>>>>
>>>>> Hi All
>>>>>
>>>>> I have generated several PMF curves for the one system using umbrella
>>>>> sampling. In the first part of the curve (barrier region) I use a high
>>>>> force constant with small intervals between the windows. The latter
>>>>> part
>>>>> of the curve I use a lower force constant with larger window spacing.
>>>>> Anyway I have a few issues that I need clarifying:
>>>>> 1 - Can you have too much overlap between windows?
>>>> no, there no such a thing of too much overlap :)) You could even put
>>>> two identical windows with same 100% overlap ... no problem.
>>>>> 2 - Does the distribution at each window have to centered around the
>>>>> desired r0? (If not does this affect the free energy?)
>>>> The deviation of the distribution from the r0 is what dictates the
>>>> profile. The more away from the disired r0 the higher the free energy
>>>> of the system.
>>>>> 3- If you over sample one particular window, will it affect the curve?
>>>> There is no such a thing of over sampling ... the only thing you can
>>>> have is not enough sampling.
>>>>> Many thanks
>>>>>
>>>>> GAvin
>>>>> -- 
>>>>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> -- 
>>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 

-- 
========================================

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

========================================