[gmx-users] Umbrella Sampling tutorial

[shahab shariati]

Dear Justin

My system contains lipid bilayer + drug + water molecules.

I want to calculate Potential of mean force as a function of the
distance between the centers of mass of drug and the lipid bilayer.

Based on your suggestion I used pull_geometry = position for my case.

After the minimization and equilibration, for Generating Configurations
step, I used following parameters in the md-pull.mdp file:
----------------------------------------------------------------------
title               = md-pull
; Run parameters
integrator       = md
nsteps           = 500000
dt                 = 0.002
; Output control
nstxout          = 1000
nstvout          = 1000
nstxtcout       = 1000
nstenergy       = 1000
nstlog            = 1000
energygrps      = CHOL DOPC drg SOL
; Bond parameters
continuation    = yes
constraint_algorithm = lincs
constraints      = all-bonds
lincs_iter         = 1
lincs_order      = 4
; Neighborsearching
ns_type          = grid
nstlist            = 5
rlist                = 1.0
rcoulomb         = 1.0
rvdw               = 1.0
; Electrostatics
coulombtype    = PME
pme_order       = 4
fourierspacing   = 0.16
; Temperature coupling is on
tcoupl             = V-rescale
tc-grps            = CHOL_DOPC    drg SOL
tau_t              = 0.5    0.5       0.5
ref_t               = 323     323       323
; Pressure coupling is on
pcoupl             = Berendsen
pcoupltype       = semiisotropic
tau_p              = 2.0
ref_p               = 1.0    1.0
compressibility   = 4.5e-5    4.5e-5
; Periodic boundary conditions
pbc                  = xyz
; Dispersion correction
DispCorr           = EnerPres
; Velocity generation
gen_vel             = no
; COM motion removal
nstcomm           = 1
comm-mode       = Linear
comm-grps        = CHOL_DOPC_drg  SOL
; Pull code
pull                  = umbrella
pull_geometry    = position
pull_dim            = N N Y
pull_start          = yes
pull_ngroups      = 1
pull_group0        = CHOL_DOPC
pull_group1        = drg
pull_rate1          = 0.01
pull_k1              = 1000
pull_init1           = 0
pull_vec1           = 0 0 1
---------------------------------------------------------------------------------

Then I used following tools:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
pull.tpr
mdrun -s pull.tpr

pull.gro file was not created and there are strange pdb files with names:

step240702b_n0.pdb
step240702c_n0.pdb
step240704b_n0.pdb
step240704c_n0.pdb
step240706b_n0.pdb
step240706c_n0.pdb
step240707b_n0.pdb
step240707c_n0.pdb
step240708b_n0.pdb
step240708c_n0.pdb
step240709b_n0.pdb
step240709b_n1.pdb
step240709c_n0.pdb
step240709c_n1.pdb

While, there should be obtained 500 frames. I saw one of these pdb files by
VMD,
(step240708c_n0.pdb). I attached figure related to this pdb in below link:

https://www.dropbox.com/s/6qnn4okv63qieec/pdb%20file.docx

When I use trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep, only 241 gro
files
were created from conf0.gro to conf240.gro instead of 501 gro files.

I used same parameters in mdp file except Pull code parameters
for simulation of my system for 20 ns and there are no problems.

What is the reason of this state? Is my Pull code parameters wrong?

Any help will highly appreciated.