Also, you may want to check that your rcoulomb and rvdw values are
correct...  Didn't look at your mdp files until just now.  Why are they set
to zero?

On 29 November 2016 at 16:56, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> 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 <sli...@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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>
>
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
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>
>


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