From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Feb 14 2014 - 07:34:46 CST
no, it won't affect the "final" result. But it may be the difference
between reaching equilibrium within a billion steps, and reaching it within
a trillion. In the end, you want to see the simulation sample back and
forth along the whole reaction coordinate.
On Thu, Feb 13, 2014 at 11:50 PM, Abir Ganguly <7.someone.iitd_at_gmail.com>wrote:
> Hi Aron,
>
> Thanks for your reply. I had just one more question to you (and other NAMD
> users). Does a really high number of fullSamples effect the final result? I
> would think that as long as the fullSamples value is sufficient, increasing
> it further should not effect the final outcome (as long as you increase the
> total number of steps proportionally).
>
> Thanks again.
>
>
> Best,
>
> Abir
>
> On Feb 10, 2014, at 11:20 AM, Aron Broom <broomsday_at_gmail.com> wrote:
>
> I think ABF will not sample evenly across the reaction coordinate until
> the energy landscape has been flattened, so if the counts aren't even then
> this suggests it hasn't reached equilibrium. In particular, it looks like
> you are not sampling the energy minima well, which suggests maybe the
> fullsSamples value could be increased so that the bias is not applied
> prematurely. Keep in mind that the fullSamples, I think, it the number of
> timesteps. So assuming a 2 fs timestep, you are talking about 80 ps of
> simulation until you apply the bias. For systems such as proteins or
> nucleic acids, the decorrelation time of the coordinates can easily be on
> this same order, so while you have measured 40000 samples, you may in
> practice only have 1 or 2 unique ones, and so the bias that gets applied
> can be very far from what it "ought" to be, and then it can be a very long
> road to correcting that initial mistake.
>
> Umbrella sampling obviously avoids the above issue, since you can choose
> where to invest more simulation time if you want.
>
>
>
>
> On Sat, Feb 8, 2014 at 4:38 PM, Abir Ganguly <7.someone.iitd_at_gmail.com>wrote:
>
>> Dear NAMD users,
>>
>> I have been trying to calculate the PMF along a particular angle
>> coordinate in a relatively small RNA system. The angle is a heavy
>> atom-hydrogen-heavy atom angle, and spans from ~50 to ~180 degrees. I am
>> trying to do it in two different ways, using ABF simulations and umbrella
>> sampling simulations.
>> In the case of ABF, I first ran for 12ns using fullsamples 40,000, and
>> then extended the simulation to 25ns. I also ran another 12ns simulation
>> starting from the end of the 25ns simulation.
>> In the case of US, I manually ran 42 windows each for over 1 ns ( 200 ps
>> equil). Attached are the pmf plots obtained from the simulations. As you
>> can see from the plot, the results from the two methods are not consistent
>> with each other. When I look at the .count file from the ABF
>> simulations(plot attached), I notice that the end points are not sampled
>> well. The qualitative similar behaviour between the 12ns and 25ns
>> simulations to me is a bit disconcerting. Just increasing the simulation
>> time may not fix the problem. I will appreciate any suggestion on how to
>> improve the sampling at the end points.
>>
>> Below is an example colvar file that I am using for the ABF simulations
>>
>> ************************************************************
>> ********************************
>>
>> colvarsTrajFrequency 100
>> colvarsRestartFrequency 1000
>> colvarsTrajAppend on
>>
>> colvar {
>> name orient
>> width 2.5
>> lowerboundary 50
>> upperboundary 180
>> lowerWallConstant 1
>> upperWallConstant 1
>> angle {
>> group1 {
>> atomnumbers 29
>> }
>> group2 {
>> atomnumbers 30
>> }
>> group3 {
>> atomnumbers 34
>> }
>> }
>> }
>>
>>
>> abf {
>> colvars orient
>> fullSamples 40000
>> inputPrefix pmf-output
>> }
>> ************************************************************
>> ******************
>>
>> Thanks for your time.
>>
>> Best,
>>
>> Abir<jpg.pmfs_low.jpeg><jpg.counts.abf_low.jpeg>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:07 CST