[gmx-users] gmx wham problem

[edesantis]

do you have any suggestions???

thanks
Emiliano

On 2017-07-01 14:01, edesantis wrote:
> Dear Matthew,
> thanks for your opinion.
> How can you establish if the histograms are sufficiently overlapped?
> Is there any thumbs role?
> For what concern the negative sign of reaction coordinates, I think it
> could derive from the choice of the order of the pulling groups and
> the vector along you are pulling.
> 
> Thank you again
> Best regards,
> Emiliano
> 
> 
> On 2017-06-28 17:49, Thompson, Matthew White wrote:
>> It looks like you need to sample more states, 13 is not enough.
>> Probably more like 20-30+ would be needed to get a smooth PMF as is
>> discussed in that tutorial. The weird features in your PMF are from
>> insufficiently overlapping histograms, for example the bump near -2.2
>> nm corresponds to having no histogram there. You also see that you
>> only have one state near -1.2 nm, so that is probably not being
>> sampled enough for WHAM to produce meaningful results.
>> 
>> Also I don't understand the meaning of negative distance as a reaction
>> coordinate. If that is the distance between two things, maybe it
>> should be positive. It makes it difficult to understand which values
>> correspond to them being close and far away.
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of
>> edesantis [edesantis at roma2.infn.it]
>> Sent: Wednesday, June 28, 2017 10:26 AM
>> To: Gmx users
>> Subject: [gmx-users] gmx wham problem
>> 
>> dear all,
>> 
>> I am studying the affinity between an antibody and an amyloid peptide; 
>> I
>> am interested in the evaluation of the PMF. I have a problem with the
>> PFM shape.
>> I followed the protocol described in the umbrella-sampling tutorial
>> (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html)
>> Here below there is the .mdp part for the pulling
>> ; Pull code
>> pull                    = yes
>> pull_ngroups            = 2
>> pull_ncoords            = 1
>> pull_group1_name        = Chain_Abeta
>> pull_group2_name        = Chains_Antibody
>> pull_coord1_type        = umbrella      ; harmonic biasing force
>> pull_coord1_geometry    = direction
>> pull_coord1_groups      = 1 2
>> pull_coord1_vec         =  38.207 68.611 29.8493
>> pull_coord1_rate        = 0.002        ; 0.01 nm per ps = 10 nm per ns
>> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
>> pull_coord1_start       = yes           ; define initial COM distance 
>> >
>> 0
>> 
>> After the pulling simulation, I’ve extracted 13 configuration; for 
>> each
>> them, 36 ns of equilibration were performed. These are the mdp
>> directives:
>> ; Pull code
>> pull                    = yes
>> pull_ngroups            = 2
>> pull_ncoords            = 1
>> pull_group1_name        = Chain_Abeta
>> pull_group2_name        = Chains_Antibody
>> pull_coord1_type        = umbrella      ; harmonic biasing force
>> pull_coord1_geometry    = direction
>> pull_coord1_groups      = 1 2
>> pull_coord1_vec         = 38.207 68.611 29.8493
>> pull_coord1_rate        = 0.00
>> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
>> pull_coord1_start       = yes           ; define initial COM distance 
>> >
>> 0
>> 
>> Then I ran the wham command:
>> Gmx wham –it list_tpr.dat –if list_pullf.dat -v  –b 20000 –o –hist
>> And I’ve obtained the following pictures:
>> http://i66.tinypic.com/11t5zdv.png
>> http://i67.tinypic.com/30u8g8x.png
>> Do you have any idea of why the pfm profile has this strange shape?
>> Could it come from any kind of error I’ve made during the simulations?
>> If there are not errors, it seems that the configurations in which the
>> peptide is far from the antibody are more energetically favoured 
>> respect
>> to those in contact with the antibody, but I have some doubts about 
>> it…
>> 
>> Can you help me?
>> Thank you in advance,
>> best regards,
>> Emiliano
>> 
>> 
>> --
>> Emiliano De Santis
>> --
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> 
> --
> Emiliano De Santis

-- 
Emiliano De Santis