[gmx-users] energy group exclusion

[rose rahmani]

Hello;

this is md_pull.mdp

integrator               = md
dt                       = 0.002
nsteps                   = 1000000
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 500
nstlog                   = 500
nstenergy                = 1000
nstxtcout                = 1000
nstlist                  = 10
rlist                    = 1.5
cutoff-scheme            = Verlet
energygrp-excl           = WAL WAL ZnS ZnS
coulombtype              = pme
rcoulomb                 = 1.2
vdwtype                  = Switch
rvdw_switch              = 1.0
rvdw                     = 1.2
pcoupl                   = no
gen_vel                  = no
constraints              = h-bonds
ns_type                  = grid
pbc                      = xy
freezegrps               = WAL ZnS
freezedim                = Y Y Y Y Y Y
energygrps               = SOL WAL ZnS Protein NA CL
energygrp-excl           = WAL WAL ZnS ZnS
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 code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = ZnS
pull_group2_name        = Protein
pull_coord1_type        = umbrella
pull_coord1_geometry    = direction
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_coord1_vec         = 0 0 1
pull_coord1_rate        = -0.001
pull_coord1_k           = 5000
pull_coord1_start       = yes
pull_nstxout            = 10

----------------------------------------------

ERROR 1 [file md_pull.mdp]:
  Energy group exclusions are not (yet) implemented for the Verlet scheme


WARNING 1 [file md_pull.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
Pull group  natoms  pbc atom  distance at start  reference at t=0
       1       560       280
       2        26       773       1.763 nm          1.763 nm
Estimate for the relative computational load of the PME mesh part: 0.77

NOTE 3 [file md_pull.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.


This run will generate roughly 149 Mb of data

There were 3 notes

There was 1 warning

There were 3 notes

There was 1 warning

-------------------------------------------------------
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 2107

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

i implemented  energygr-excl in mdp file, so why get this error?!

and my second question is that i want to pull Protein(to get closer to
sheet) to ZnS sheet, so should i use position restraint for Protein in this
step?
and what is the difference between geometry= direction or distance in my
system?

Would you please help me?

With regards