[gmx-users] umbrella sampling
rose rahmani
rose.rhmn93 at gmail.com
Sun Nov 26 23:09:31 CET 2017
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
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