[gmx-users] Umbrella Sampling

[rose rahmani]

Hello

i'm trying to do umbrella sampling and
 this is  part of md_umbrella.mdp;
DEFINE                   = -DPOSRES
integrator               = md
dt                       = 0.001
nsteps                   = 40000000
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 5000
nstenergy                = 10000
nstxtcout                = 10000
rlist                    = 1.5
coulombtype              = pme
rcoulomb                 = 1.5
vdwtype                  = Switch
rvdw_switch              = 1.0
rvdw                     = 1.2
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
-----------------
when i use grompp i get this erro and notes;

NOTE 1 [file md_umbrella.mdp, line 52]:
  md_umbrella.mdp did not specify a value for the .mdp option
  "cutoff-scheme". Probably it was first intended for use with GROMACS
  before 4.6. In 4.6, the Verlet scheme was introduced, but the group
  scheme was still the default. The default is now the Verlet scheme, so
  you will observe different behaviour.
--------------------
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#

ERROR 1 [file md_umbrella.mdp]:
  With Verlet lists rcoulomb!=rvdw is not supported


NOTE 2 [file md_umbrella.mdp]:
  Replacing vdwtype=Switch by the equivalent combination of vdwtype=Cut-off
  and vdw_modifier=Potential-switch
----------------
i used version 4.5.4  before grompp and i think this error comes from
using  gmx,but i dont know how EXACTLY should i change mdp file when i us
gmx. (i want to move protein toward ZnS and protein is 1.5nm far from ZnS
at t=0 and both of them are in center of simulation box at t=0).

thank you so much

best regards
rose