[gmx-users] Problem in PMF simulation

[Billy Williams-Noonan]

My PMF curves look similar to that.  What you're seeing towards the end of
that curve is either an artifact of the algorithms used to model the
system, a very minor sampling problem, or a mix of both.  Your Gaussians
may be split because they are bi-modal and the most energetically
favourable position around your constraint is in two places.  Try having a
look at your individual umbrella windows to figure out what's going on. :)

Cheers,

Billy

On 29 November 2016 at 15:20, Shi Li <sli259 at g.uky.edu> wrote:

> Dear Gromacs users,
>
> I posted this question a few days ago, but still couldn’t solve it. This
> problem has bothered my for a long time, so I am reposting this for help.
>
> I am currently doing some PMF simulations for two small molecular types in
> vacuum. I applied an energy minimization, a NVT equilibrium and a
> production run on my system. Following are the mdp files for each. I used a
> commend in my run script to change the Window in pull_coord1_init in the
> pull code for each sample window.
>
> Energy minimization
> ---
> integrator               = steep
> nsteps                   = 20000
>
> nstenergy                = 500
> nstlog                   = 500
> nstxout-compressed       = 1000
>
> cutoff-scheme            = group
>
> coulombtype              = Cut-off
> rcoulomb                 = 0
>
> vdwtype                  = Cut-off
> rvdw                     = 0
> rlist                    = 0
> pbc                      = no
>
> ; Pull code
> pull             = umbrella
> pull_geometry    = distance
> pull_start       = no
> pull-ncoords     = 1
> pull_group1_name = ADT1
> pull_group2_name = ADT2
> pull-coord1-groups = 1 2
> pull_coord1_init = WINDOW
> pull_coord1_rate = 0.0
> pull_coord1_k = 5000
>
> —
> NVT
> ----
> integrator               = md
> dt                       = 0.002     ; 2 fs
> nsteps                   = 500000    ; 1.0 ns
>
> nstenergy                = 200
> nstlog                   = 2000
> nstxout-compressed       = 10000
>
> continuation             = yes
> constraint-algorithm     = lincs
> constraints              = h-bonds
>
> cutoff-scheme            = group
> rlist                    = 0
>
> rcoulomb                 = 0
>
> rvdw                     = 0
> pbc                      = no
> tcoupl                   = V-rescale
> tc-grps                  = System
> tau-t                    = 2.0
> ref-t                    = 298.15
> nhchainlength            = 1
>
> ; Pull code
> pull             = umbrella
> pull_geometry    = distance
> ;pull_dim         = N N Y
> pull_start       = no
> pull-ncoords     = 1
> pull_ngroups     = 2
> pull_group1_name = ADT1
> pull_group2_name = ADT2
> pull-coord1-groups = 1 2
> pull_coord1_init = WINDOW
> pull_coord1_rate = 0.0
> pull_coord1_k = 5000
>
> ——
> Production run:
> ----
> integrator               = md
> dt                       = 0.002   ; 2 fs
> nsteps                   = 10000000   ; 20.0 ns
>
> nstenergy                = 5000
> nstlog                   = 5000
> nstxout-compressed       = 5000
>
> continuation             = yes
> constraint-algorithm     = lincs
> constraints              = h-bonds
>
> cutoff-scheme            = Group
>
> rcoulomb                 = 0
> rlist                    = 0
>
> rvdw                     = 0
> pbc                      = no
>
> tcoupl                   = V-rescale; Nose-Hoover
> tc-grps                  = System
> tau-t                    = 2.0
> ref-t                    = 298.15
> nhchainlength            = 1
>
> ; Pull code
> pull             = umbrella
> pull_geometry    = distance
> pull_start       = no
> pull-ncoords     = 1
> pull_ngroups     = 2
> pull_group1_name = ADT1
> pull_group2_name = ADT2
> pull-coord1-groups = 1 2
> pull_coord1_init = WINDOW
> pull_coord1_rate = 0.0
> pull_coord1_k = 5000
>
> ———
> I have a very strange profile and histogram. I uploaded to these links.
>
> PMF: https://www.dropbox.com/s/i10hn1p30w2j71r/F-anti-adt.eps?dl=0
> HISTO: https://www.dropbox.com/s/1xi9i4cj60g97n2/F-anti-histo.eps?dl=0
>
> The molecule is about 1.5 nm long, so the smooth profile before 1.5 nm
> looks fine, but I don’t understand why the profile had this fluctuation
> after 1.5 nm and the histogram seems to have some split peaks after this
> length. Can anyone tell me why this happened? Is there something wrong in
> my mdp file or something wrong in my topology? I have used this similar mdp
> files for my other types of molecular systems and the results were fine. So
> it is really confused me now.
>
> I appreciate for any help! Thanks!
>
> Shi
>
>
>
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