[gmx-users] WHAM

[Roja]

Why you don't answer me?is there anything wrong in my question?
Thank you

Sent from my iPhone

> On Dec 17, 2017, at 17:36, rose rahmani <rose.rhmn93 at gmail.com> wrote:
> 
> Hi,
> 
> I try to use umbrella sampling for calculating PMF. i change distance
> between protein and ZNS nanosheet. I use gomacsV4.5.4
> 
> after minimization and equilibration. i use:
> 
> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
> 
> this is md_pull.mdp:
> 
> integrator               = md
> dt                       = 0.002
> nsteps                   = 1000000
> nstxout                  = 5000
> nstvout                  = 5000
> nstfout                  = 500
> nstlog                   = 500
> nstenergy                = 1000
> nstxtcout                = 1000
> nstlist                  = 10
> rlist                    = 1.5
> coulombtype              = pme
> rcoulomb                 = 1.5
> vdwtype                  = Switch
> rvdw_switch              = 1.0
> rvdw                     = 1.2
> pcoupl                   = no
> gen_vel                  = no
> constraints              = h-bonds
> ns_type                  = grid
> pbc                      = xy
> freezegrps               = WAL ZnS
> freezedim                = Y Y Y Y Y Y
> energygrp-excl           = WAL WAL ZnS ZnS
> energygrps               = SOL WAL ZnS Protein NA CL
> nwall                    = 2
> wall-atomtype            = C C
> wall-type                = 9-3
> wall-density             = 150 150
> wall-ewald-zfac          = 3
> ewald-geometry           = 3dc
> fourierspacing           = 0.12
> tcoupl                   = v-rescale
> tc-grps                  = System
> tau-t                    = 0.1
> ref-t                    = 300
> 
> ; Pull code
> pull                    = umbrella
> pull_ngroups            = 1
> pull_group0             = ZnS
> pull_group1             = Protein
> pull_geometry           = direction
> pull_vec1               = 0 0 1
> pull_dim                = N N Y
> pull_rate1              = -0.01
> pull_k1                 = 5000
> pull_start              = yes
> pull_nstxout            = 50
> 
> then: mdrun -s pull.tpr
> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
> 
> i got 1000 configuration, i selected 27 of them and foe each of them i run
> md_umbrella.mdp
> 
> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top
> -n index.ndx -o umbrella0.tpr and then:
> 
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
> 
> 
> .This is md_umbrella.mdp file:
> 
> ntegrator               = md
> dt                       = 0.002
> nsteps                   = 2000000
> nstxout                  = 5000
> nstvout                  = 5000
> nstfout                  = 500
> nstlog                   = 500
> nstenergy                = 1000
> nstxtcout                = 1000
> nstlist                  = 10
> rlist                    = 1.5
> coulombtype              = pme
> rcoulomb                 = 1.5
> vdwtype                  = Switch
> rvdw_switch              = 1.0
> rvdw                     = 1.2
> pcoupl                   = no
> gen_vel                  = no
> constraints              = h-bonds
> ns_type                  = grid
> pbc                      = xy
> freezegrps               = WAL ZnS
> freezedim                = Y Y Y Y Y Y
> energygrp-excl           = WAL WAL ZnS ZnS
> energygrps               = SOL WAL ZnS Protein NA CL
> nwall                    = 2
> wall-atomtype            = C C
> wall-type                = 9-3
> wall-density             = 150 150
> wall-ewald-zfac          = 3
> ewald-geometry           = 3dc
> fourierspacing           = 0.12
> tcoupl                   = v-rescale
> tc-grps                  = System
> tau-t                    = 0.1
> ref-t                    = 300
> 
> pull                    = umbrella
> pull_ngroups            = 1
> pull_group0             = ZnS
> pull_group1             = Protein
> pull_geometry           = direction
> pull_vec1               = 0 0 1
> pull_dim                = N N Y
> pull_rate1              = 0.0        ; 1 nm per  ns
> pull_k1                 = 5000
> pull_start              = yes
> pull_nstxout            = 50
> ...........................................................
> 
> then i use :
> 
> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> 
> 
> i get histo.xvg and profile.xvg file but the profile.xvg contains nan
> vavlue. i don't know why?
> 
> 
> # This file was created Wed Dec 13 14:54:35 2017 # by the following
> command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> # # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
> Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
> (kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
> -nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00
> -nan 1.265638e+00 -nan
> 
> .
> 
> .
> 
> .
> 
> .
> 
> 
> Would you please help me? i have not encounter this problem before
> 
> and also i want protein get closer to ZnS sheet during pulling in just
> Z direction and straightforward to sheet( like one straight line to
> sheet), is this suitable md_pull.mdp file for this approach? and what
> about time?is 4nS suitable for each window?is it possible at all?
> 
> Would you please help me?
> 
> 
> Best regards
> 
> Rose
> -- 
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