[gmx-users] PMF of a short peptide on a solid surface

[Alexander Alexander]

Dear gromacs user,

In order to simulate the PMF of a adsorbed short peptide on a solid
surface, first I minimised and equlibrated(NVT and NPT) the system and then
I did a 60 ns of production run in which the peptide fully adsorbed to the
surface. I used these out put to pull away the peptide from the surface
using below mdp file (to produced required trajectory for generating
configuration):
+++++++++++++++
title                    = C16-Slab-Water-Na
integrator               = md
dt                            = 0.001     ; 1 fs
nsteps                    = 10000000   ; 10 ns
xtc-precision          = 2000

nstenergy                = 5000
nstlog                       = 5000
nstxout-compressed       = 1000
nstxout                  = 1000
nstlist                  = 40

continuation             = yes
gen-vel                  = no
;gen-temp                 = 298.15
;gen-seed                 = 173529

constraint-algorithm     = lincs
constraints              = h-bonds

cutoff-scheme            = Verlet

coulombtype              = PME
rcoulomb                 = 1.3
vdwtype                  = Cut-off
rvdw                     = 1.3
DispCorr                 = EnerPres

tcoupl                   = Nose-Hoover      ;v-rescale  ;berendsen
tc-grps                  = Protein Non-Protein
tau-t                    = 1.61     1.61
ref-t                    = 298.15  298.15
nhchainlength            = 1
pbc                      = xyz

pcoupl                   = no
energygrps                = Protein Slab Water_and_ions

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-start        = yes
pull-coord1-rate         = 0.001          ;;;0.007
pull-coord1-vec          = 0.0 0.0 1.0
pull-coord1-geometry     = direction-periodic
pull-coord1-k            = 500               ;;;1000
pull-print-components    = Yes
++++++++++++++++

Although I do not use hard spring (500 and 1000) and fast pulling
rate(0.001 and 0.007) but I do not know why the peptide suddenly pulled
away from the slab in the second or third frame?

Thanks.
Alex