Why is my ABF simulation sampling from a small set of values?
wisecashew opened this issue · 2 comments
I am running a simulation of a polymer in water. I am trying to calculate the free energy of the radius of gyration using ABF. I am using LAMMPS. I would like an F(Rg) curve as 5<=Rg<=30, but the ends can be flexible.
This is my input file for the simulation:
Colvarstrajfrequency 1000
Colvarsrestartfrequency 20000
colvar {
name my_rg
gyration {
atoms { atomNumbersRange 1-572 }
}
lowerBoundary 5.0
upperBoundary 30.0
# width=0.5
}
harmonicWalls {
name wall
colvars my_rg
lowerWalls 5.0
upperWalls 30.0
lowerWallConstant 25.0
upperWallConstant 25.0
}
abf {
name abf_r
colvars my_rg
outputFreq 5000
fullSamples 1000
historyFreq 50000
}
On running the simulation, I looked at out.pmf file and I see:
# 1
# 4.50000000000000e+00 1.00000000000000e+00 26 0
5.00000000000000e+00 1.20005097266126e+02
6.00000000000000e+00 1.20005097266126e+02
7.00000000000000e+00 1.20005097266126e+02
8.00000000000000e+00 1.20005097266126e+02
9.00000000000000e+00 2.81986236616591e+01
1.00000000000000e+01 0.00000000000000e+00
1.10000000000000e+01 0.00000000000000e+00
1.20000000000000e+01 0.00000000000000e+00
1.30000000000000e+01 0.00000000000000e+00
1.40000000000000e+01 0.00000000000000e+00
1.50000000000000e+01 0.00000000000000e+00
1.60000000000000e+01 0.00000000000000e+00
1.70000000000000e+01 0.00000000000000e+00
1.80000000000000e+01 0.00000000000000e+00
1.90000000000000e+01 0.00000000000000e+00
2.00000000000000e+01 0.00000000000000e+00
2.10000000000000e+01 0.00000000000000e+00
2.20000000000000e+01 0.00000000000000e+00
2.30000000000000e+01 0.00000000000000e+00
2.40000000000000e+01 0.00000000000000e+00
2.50000000000000e+01 0.00000000000000e+00
2.60000000000000e+01 0.00000000000000e+00
2.70000000000000e+01 0.00000000000000e+00
2.80000000000000e+01 0.00000000000000e+00
2.90000000000000e+01 0.00000000000000e+00
3.00000000000000e+01 0.00000000000000e+00
It seems like only integer values less than 9 have been sampled. Furthermore, if I look at out.count:
# 1
# 5.00000000000000e+00 1.00000000000000e+00 25 0
5.50000000000000e+00 0
6.50000000000000e+00 0
7.50000000000000e+00 0
8.50000000000000e+00 12040750
9.50000000000000e+00 7959250
1.05000000000000e+01 0
1.15000000000000e+01 0
1.25000000000000e+01 0
1.35000000000000e+01 0
1.45000000000000e+01 0
1.55000000000000e+01 0
1.65000000000000e+01 0
1.75000000000000e+01 0
1.85000000000000e+01 0
1.95000000000000e+01 0
2.05000000000000e+01 0
2.15000000000000e+01 0
2.25000000000000e+01 0
2.35000000000000e+01 0
2.45000000000000e+01 0
2.55000000000000e+01 0
2.65000000000000e+01 0
2.75000000000000e+01 0
2.85000000000000e+01 0
2.95000000000000e+01 0
It seems to confirm that only about Rg from 8-9 are being sampled.
I decided to restart the run using the previous state file and this input file:
Colvarstrajfrequency 1000
Colvarsrestartfrequency 20000
colvar {
name my_rg
gyration {
atoms { atomNumbersRange 1-572 }
}
lowerBoundary 5.0
upperBoundary 30.0
# width=0.5
}
harmonicWalls {
name wall
colvars my_rg
lowerWalls 5.0
upperWalls 30.0
lowerWallConstant 25.0
upperWallConstant 25.0
}
abf {
name abf_r
# inputPrefix out
colvars my_rg
outputFreq 5000
fullSamples 1000
historyFreq 50000
}
But I see no improvements in the values that are being sampled. How do I improve the sampling from the simulation? Are there any ways to tweak the force parameters for better sampling? I am running metadynamics simulations using PLUMED to check that both Free Energy Surfaces match, and as is it stands, it seems like the ABF is simply not sampling well enough.
I would greatly appreciate any advice you have for me!
I think the grid on which you discretize the free energy is too coarse, so the ABF bias cannot do its job. You need to make the "width" parameter of your collective variable smaller.
@wisecashew I hope that changing the width parameter was useful. Although it's unlikely that ABF and metadynamics would yield significantly different results, do keep in mind that there is a metadynamics implementation for Colvars as well:
https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvarbias_meta