[gmx-users] semiisotropic pcoupltype in PMF pull

Alexander Alexander alexanderwien2k at gmail.com
Fri Aug 12 15:16:14 CEST 2016

Dear gromacs user,

In my normal MD simulation of adsorption of a short peptide into a solid
surface in water solution, my system is nicely equilibrating (after 1.5 ns
NPT using isotropic condition) to an average around 1 bar pressure which is
my desire.

However, in my PMF calculations in which I try to pull away peptide from
solid surface in the Z direction, first of all, the PBC problem forced me
to use the "direction-periodic" instead of "direction" and then
"semiisotropic" with zero compressibility in the Z direction instead of
"isotropic". Below is my pull keywords. These changes respect to my normal
MD causes not to reach to equilibration of 1 bar pressure after 1.5 ns, in
each window, but the pressure average  is around -500 like below in one

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Pressure                   -591.237        1.7     255.97   -8.49498  (bar)

or in another window is would be like:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Pressure                    127.992       0.97    199.158   -4.91034  (bar)

Another window:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Pressure                   -273.501       0.34    201.917   0.521768  (bar)

Would you please let me know if the pressures are fine or I should increase
the time of NPT equilibration more than 1.5 ns?

pcoupl                       = berendsen
Pcoupltype               = semiisotropic       ;*****
tau_p                         = 2.5
compressibility          = 4.46e-5  0.0        ;*****
ref_p                           = 1.0  1.0
refcoord-scaling        = com

pull                               = yes
pull-ngroups                = 2
pull-ncoords                 = 1
pull-group1-name        = Protein
pull-group2-name        = Slab

pull-coord1-groups       = 1 2
pull-coord1-type            = umbrella
pull-coord1-dim             = N N Y
pull-coord1-init              = WINDOW
pull-coord1-start            = no
pull-coord1-rate             = 0.0
pull-coord1-vec              = 0.0 0.0 1.0               ;*****
pull-coord1-geometry    = direction-periodic   ;*****
pull-coord1-k                  = 5000
pull-print-components    = Yes

Also, If the my entries for the pull code are fine? any suggestion in this
system, please?

Thanks in advance.


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