[gmx-users] Re: PMF in vacuum (chris.neale at utoronto.ca)

[Eudes Fileti]

Hello Chris, thanks for your attention.
I'm sending you some links to some tests
I performed. As I said you will notice that
depending on the parameter used my simulation
shows PMF profiles quite different. Especially what
concerns to the difference between the use or not of the PBC.

https://sites.google.com/site/fileti/files/test1.jpg
https://sites.google.com/site/fileti/files/test2.jpg
https://sites.google.com/site/fileti/files/histo.png

I have constructed two very similar topologies (ben-a.itp and ben-b.itp)
where I put a virtual site in the center of benzene.
This sites were restrained to keep my molecules
fixed distance desired.

The basic details of the simulations are given below:1000

define                   = -DPOSRES
integrator               = sd
tinit                    = 0
dt                       = 0.002
nsteps                   = 5000000 or 500000
comm-mode                = angular
nstcomm                  = 1
comm-grps                = System
bd-fric                  = 1
ld-seed                  = 1993
nstlist                  = 5
ns_type                  = simple
pbc                      = no or xyz
periodic_molecules       = no
rlist                    = 0
coulombtype              = Cut-off
vdw-type                 = Cut-off
rvdw                     = 0
DispCorr                 = no
Tcoupl                   = Nose-Hoover
tc_grps                  = system
tau_t                    = 0.1
ref_t                    = 300
Pcoupl                   = no
pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
constraints              = all-bonds
constraint_algorithm     = lincs

; COM PULLING
pull                     = umbrella
pull_geometry            = distance
pull_dim                 = N N Y
pull_r1                  = 1
pull_r0                  = 1.5
pull_constr_tol          = 1e-06
pull_start               = yes
pull_nstxout             = 10
pull_nstfout             = 10
pull_ngroups             = 1
pull_group0              = BENa
pull_weights0            =
pull_pbcatom0            = 0
pull_group1              = BENb
pull_weights1            =
pull_pbcatom1            = 0
pull_vec1                = 0 0 1
pull_init1               = 0
pull_rate1               = 0.0
pull_k1                  = 1700 or

_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br



> Dear Eudes:
>
> Can you please elaborate on your description? What .mdp options are
> you using? What exactly do your curves look like (you can post
> pictures to photobucket or some other online service and link them
> here)? If you suspect that you are doing something wrong, then we need
> to understand exactly what you are doing and exactly what you are
> seeing in order to help.
>
> Chris.
>
> -- original message --
>
> Hi gmx-users,
> I'm trying to simulate a umbrella sampling PMF between two benzene
> molecules
> in vacuum. My protocol is working fine, my histograms have good overlap and
> the curves I have got are quite reasonable.
>
> However I have noticed that some options in my .mdp file can significantly
> change
> the depth of the well. Also the curves can not go to zero at long
> distances.
> For example, if I use PBC I get a reasonably good value for the minimum of
> the PMF
> but from a certain separation it starts to increase slightly in a linear
> fashion
> instead of going to zero. On the other hand, if I make pbc = no, I get an
> acceptable curve,
> with the PMF going to zero, but with the minimum too high.
>
> Someone could give me any tips on the best set of parameters to calculate
> this PMF in a vacuum?
> bests
> eef
>
>
>
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