[gmx-users] umbrella histograms

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Aug 12 23:29:18 CEST 2010

Dear Gavin:

plot the position vs. time. Probably you will see it sample around one  
value, then discover a new state, and make a sharp transition to  
another value. If the new state is much more favourable than the  
initial state, then you can discard the initial state as  
equilibration. It might not be though...

Also, could you have a PBC problem? I suggest that you read up on  
pull_pbcmol and try some tests with smart values of pull_pbcmol.


-- original message --

Hi all

  I am generating a potential of mean force curve for the interaction
between two cage molecules using umbrella sampling. The system is
composed of only the two molecules in question, using no pbc and no
cut-offs. Umbrella sampling is performed at 25 different distances
(between COMs) between 0.75 and 2.75 nm.  The histogram generated form
g_wham shows very good overlap between the histogram between 0.75 nm and
2 nm. The shapes of the histogram and the width of the distribution are
all well in this region. Above 2nm the histograms show two peaks and
therefore the shape and distribution at these distances is poor. Has
anyone ever come across this sort of behaviour before? Also can you use
different force constants for the harmonic potential at different
distances ?



p.s Here is a copy of the mdp file that I am using

title       = Pull test
cpp         =
include     =
define      =
integrator  = md
nsteps      = 50000000
dt          = 0.002
nstxout     = 250000
nstvout     = 250000
nstlog      = 250000
nstenergy   = 5000
nstfout     = 250000
pbc         = no
nstlist     = 10
ns_type     = simple
vdwtype     = cut-off
rlist       = 0
rvdw_switch = 0
rvdw        = 0
coulombtype = cut-off
rcoulomb    = 0
tcoupl      = nose-hoover
tc_grps     = system
tau_t       = 0.1
ref_t       = 600
gen_vel     = no
gen_temp    =
constraints = none
comm_mode   = angular
pull        = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_init1 = 2.59
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000

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