[gmx-users] umbrella sampling

[Shaoqi Zhan]

??Hi gmx-users,


I am running umbrella sampling according to the gromacs tutorial written by Justin A. Lemkul. In my system, there are two molecules (Chain_A and Chain_B) immobilized on the CNT surface with pi-stacking. I would like to calculate PMF of these two molecules (on the CNT surface) by using umbrella sampling, which means the CNT will be restrained and run umbrella sampling for two molecules (restrain one of molecules, then pull another molecule to move on the CNT surface). I use the .mdp file as follow:


title       = Umbrella pulling simulation
define      = -DPOSRES  ; position restraint the cnt
; Run parameters
integrator  = md
dt          = 0.001
tinit       = 0
nsteps      = 100000    ;
nstcomm     = 10
; Output parameters
nstxout     = 5000      ;
nstvout     = 5000
nstfout     = 500
nstxtcout   = 500       ;
nstenergy   = 500
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl      = Nose-Hoover
tc_grps     = System
tau_t       = 0.5
ref_t       = 300
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel     = no
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull                    = yes
pull_ngroups            = 3
pull_ncoords            = 1
pull_group1_name        = CNT
pull_group2_name        = Chain_A
pull_group3_name        = Chain_B
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups      =  2 3
pull_coord1_dim         = Y Y Y
pull_coord1_rate        = 0.005          ; 0.005 nm per ps = 1 nm per ns
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0

no matter which ''pull_coord1_dim'' I use (Y N N or the others), decrease timestep from 2fs to 1fs or decrease the force tolerance values from 1000 to 100 in .mdp file of minimization. I always meet an fatal error "step 216: Water molecule starting at atom 2453 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate."
And when I run regular MD simulation with gromacs for this system, it doesn't meet any error. But when I run umbrella sampling, it alsways meet an error at step of generate configurations. Could you please help me solve this problem?  Thanks.

Best,
Shaoqi Zhan