[gmx-users] energy group exclusion
rose rahmani
rose.rhmn93 at gmail.com
Sun Jan 14 15:59:22 CET 2018
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
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