[gmx-users] Umbrella sampling
gmelaugh01 at qub.ac.uk
Thu Mar 31 12:20:14 CEST 2011
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.
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
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