GROMACS version:
GROMACS modification: No
Dear users,
Consider the setup of a simulation box shown in attached image file. Box contains vapor-liquid interface, and consists of water and monoethanolamine (a small molecule) molecules. PBC is applied in all three directions.
I wish to move a monoethanolamine molecule (let’s call it my_MEA) across the box along the Z-axis and plot the potential mean force (PMF), which will look something as shown in the attached figure. Can anyone kindly provide an MDP file for doing this.
Additionally, I wish to do this using both umbrella sampling and AWH methods. Two MDP files for both the methods will be great.
In particular, I am confused about the following options:
- pull-coord1-geometry: should I use distance or direction or direction-periodic.
- pull-group1-pbcatom: Should I use -1 to turn on the cosine weighting.
- Can I use pull_group1_name = System, and pull_group2_name = my_MEA.
After reading the manual and related articles, I have come up with the following options. Can someone please verify if these options are correct.
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull-group1-pbcatom = -1 ; -1 means turn on the cosine weighting
pull_group1_name = System
pull_group2_name = my_MEA
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = no
pull-coord1-type = external-potential ;umbrella
pull-coord1-potential-provider = awh
awh = yes
awh-nbias = 1
awh1-ndim = 1
awh1-dim1-coord-index = 1
;5.49102 5.49102 16.47306
awh1-dim1-start = 0
awh1-dim1-end = 3.5
awh1-dim1-force-constant = 12800
awh1-dim1-diffusion = 5e-5
awh1-error-init = 10
awh-share-multisim = yes
awh1-share-group = 1
awh1-equilibrate-histogram = yes
awh-nstout = 40000