[gmx-users] umbrella histograms

[Gavin Melaugh]

Dear Chris

Thanks but  I am not using periodic boundary conditions as I want to
simulate the two molecules in a vacuum.

Gavin

chris.neale at utoronto.ca wrote:
> 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.
>
> Chris.
>
> -- 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 ?
>
> Cheers
>
> Gavin
>
> 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
>
>
>