AWH with user data

User discussions
1

GROMACS version: 2020.3
GROMACS modification: Yes

Hi,
I’d like to test AWH with switch awh-user-data but I can’t figure out how the awhinit.xvg file should look.
I’d like to pull molecule through DPPC membrane having this pull and awh part in .mdp:

pull = yes
pull-nstfout = 100
pull-nstxout = 100

pull_ngroups = 1
pull_ncoords = 2
pull_group1_name = POPC
pull_group2_name = NEO

pull_coord1_geometry = cylinder
pull-cylinder-r = 2.0
pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull-coord1-type = external-potential ; Apply the bias using an external module.
pull-coord1-potential-provider = AWH ; The external module is called AWH!

awh = yes
awh-nbias = 1
awh1-ndim = 1
awh1-dim1-coord-index = 1
awh1-dim1-start = -2.0
awh1-dim1-end = 2.0
awh1-dim1-force-constant = 8000
awh1-dim1-diffusion = 5e-5
awh1-error-init = 5
awh1-user-data = yes

And I’d like to provide data from previous US simulations (if I understand well how these user data files should work). Something like:

gmx_mpi_sse2 wham -it tpr_files.dat -if pullf_files.dat -o hist -unit kJ

@TYPE xy
-2.223479e+00 0.000000e+00
-2.202096e+00 -1.147559e-01
-2.180713e+00 -2.216550e-01
-2.159330e+00 -3.112396e-01
-2.137947e+00 -4.310974e-01
-2.116564e+00 -5.627429e-01
-2.095182e+00 -7.274257e-01
-2.073799e+00 -9.200238e-01
-2.052416e+00 -1.141194e+00
-2.031033e+00 -1.199421e+00…

First, grompp complains it wants 3 columns. What should be in the third column? Can I get it from US? Then I also get these errors:

Error in user input:
awhinit.xvg does not contain data for all coordinate values. Make sure your
input data covers the whole sampling domain and is correctly formatted.

Error in user input:
Target distribution weight at point 0 (-0.114756) in awhinit.xvg is negative.

Please, could somebody provide me (us) working example of awh with user data?

Have a nice day.

Ondrej Kroutil
2

You should have gotten this message:

        "%s is expected in the following format. "
        "The first ndim column(s) should contain the coordinate values for each point, "
        "each column containing values of one dimension (in ascending order). "
        "For a multidimensional coordinate, points should be listed "
        "in the order obtained by traversing lower dimensions first. "
        "E.g. for two-dimensional grid of size nxn: "
        "(1, 1), (1, 2),..., (1, n), (2, 1), (2, 2), ..., , (n, n - 1), (n, n). "
        "Column ndim +  1 should contain the PMF value for each coordinate value. "
        "The target distribution values should be in column ndim + 2  or column ndim + 5. "
        "Make sure the input file ends with a new line but has no trailing new lines."

So you are missing the target distribution in the third column. With default settings, use 1 for all values.

The range should at least cover the min to max you specified in the awh mdp options.