[gmx-users] WHAM

[rose rahmani]

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