Why FES calculated from meta-eabf is not smooth as that from WT-meta?

[Wei Zhang]

Dear all,

Recentlty, I was using Plumed-2v.6 with Lammps to calculate the PMF. The coordination number is CV, both WT-meta and meta-eabf method were used. However, I found the PMF calculated from calculated from meta-eabf is not smooth as that from WT-meta. Here follows the input scripts of these method and the output PMF figures. 

1. Could anyone tell me how to change meta-eabf parameters to make the PMF line smooth?

2. How to estimate the error in free-energies with meta-eabf method?

#=========================meta-eabf=================

DRR ...

  LABEL=eabf

  ARG=ncoord

  FULLSAMPLES=500

  GRID_MAX=1.1

  GRID_MIN=0.0

  GRID_SPACING=0.02

  FRICTION=8.0

  TEXTOUTPUT

  OUTPUTFREQ=5000

  HISTORYFREQ=100000

  TAU=0.5

  TEMP=673

...

METAD ...

   LABEL=mtd

   ARG=eabf.ncoord_fict 

   SIGMA=0.1

   GRID_MAX=3.0

   GRID_MIN=-0.2

   GRID_SPACING=0.02

   HEIGHT=0.6

   PACE=1000

   TEMP=673

   BIASFACTOR=8

...

uwalls: UPPER_WALLS ARG=eabf.ncoord_fict AT=1.10  KAPPA=1000000 

lwalls: LOWER_WALLS ARG=eabf.ncoord_fict AT=0.00  KAPPA=1000000

#===================================meta========================

METAD ...

   LABEL=mtd

   ARG=ncoord

   SIGMA=0.1

   GRID_MAX=2.0

   GRID_MIN=0

   GRID_SPACING=0.02

#   GRID_BIN=50 

   HEIGHT=0.6

   PACE=1000

   TEMP=673

   BIASFACTOR=20

   CALC_RCT

   RCT_USTRIDE=10

...

#==================================================================

[Haohao Fu]

Hi, 

I noticed that you were using a similar Gaussian size for the MtD and WT-Meta-eABF simulations. I suspect that you want to use a smaller size for the WT-Meta-eABF simulation, as the biases from the ABF should dominate, and the MtD part only helps to guarantee a normal distribution of the sampling along the CV.

Good luck,

Haohao

[Victor Hue]

Dear Zhang,

Hi Zhang. I'm learning how to use PLUMED in LAMMPS at the moment. I'm using the umbrella sampling method for my research.

Since you are using LAMMPS too, do you have any idea how can I use umbrella sampling in LAMMPS? From what I know, I have to run the simulations of each bias potential in parallel for different window stages, and from the trajectory produced, I need to combine all trajectories together, and run the simulation again with all the bias potentials.

I'm not sure how can I implemented this in LAMMPS. Specifically, how to run all simulation in parallel and how to combine the trajectories in LAMMPS.

Appreciate if you know anything about this. Thanks!

Regards,

Victor

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/380ea5f9-4e04-4809-8464-f296325914a6n%40googlegroups.com.

[Wei Zhang]

Dear Victor,

there are some examples of using lammps to do umbrella sampling with wham in the pdf file contained in the website(https://sites.udel.edu/it-rci/2018/02/28/applications-of-high-performance-computing-in-geochemistry/). Hope it will helps. (The pdf file is too larger to upload here.)

Good luck,

Wei

[Victor Hue]

Dear Zhang,

Thanks for the website provided. I'm actually referring to the umbrella sampling using the PLUMED module (I'm currently using LAMMPS colvars module too) and try to compare both results. Thanks anyway!

Regards,
Victor

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/c0483295-10b3-47ba-9a4e-a55dc90e54b9n%40googlegroups.com.

[Chenghan Li]

Hi Wei,

I wonder if you used sum_hills to get the metad pmf. It uses a kernel density estimation by default which makes the pmf smooth. I am not sure about the abf thing.

Best,

Chenghan