[gmx-users] umbrella sampling

[rose rahmani]

Hi;

This is md_pull.mdp

integrator               = md
dt                       = 0.001
nsteps                   = 2000000
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 500
nstenergy                = 1000
nstxtcout                = 1000
rlist                    = 1.5
rcoulomb                 = 1.5
rvdw                     = 1.2
coulombtype              = pme
cutoff-scheme            = group
vdwtype                  = Switch
rvdw_switch              = 1.0
pcoupl                   = no
gen-vel                  = yes
gen-temp                 = 0
gen-seed                 = 173529
constraints              = h-bonds
pbc                      = xy
freezegrps               = WAL ZnS
freezedim                = Y Y Y Y Y Y
energygrp-excl           = WAL WAL ZnS ZnS
energygrps               = SOL WAL ZnS Protein NA CL
nwall                    = 2
wall-atomtype            = C C
wall-type                = 9-3
wall-density             = 150 150
wall-ewald-zfac          = 3
ewald-geometry           = 3dc
fourierspacing           = 0.12
tcoupl                   = v-rescale
tc-grps                  = System
tau-t                    = 0.1
ref-t                    = 300
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = ZnS
pull_group2_name        = Protein
pull_coord1_type        = umbrella
pull_coord1_geometry    = distance
pull_coord1_groups      = 1 2
pull__coord1_dim                = N N Y
pull_coord1_rate              = -0.001        ; 1 nm per  ns
pull_coord1_k                 = 5000
pull_coord1_start              = yes

Program gmx grompp, VERSION 5.1.4

Fatal error:
Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
times the box size (2.000000).
You might want to consider using "pull-geometry = direction-periodic"
instead.

the box size is= 4 4 12

could you please help me to resolve it?
-----
Mr.Lemkul told me rcutt-off is wrong and

 i should'nt put "cutoff-scheme            = group" >>>but when i remove
it i'll get  this error too;

  >>With Verlet lists rcoulomb!=rvdw is not supported

i know it's wrong solution but what is my alternative?!!

------
-dummy particle should move towards the surface with a constant speed of 1
nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
corresponding to the spring constant of 5000.

I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to
it?!

thank you so much

Best regards
Rose