ABF simulations

From: Abir Ganguly (7.someone.iitd_at_gmail.com)
Date: Sat Feb 08 2014 - 15:38:01 CST

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.



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