[gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Hi,

I have completed pulling as per the tutorial stated. But having a strange
issue during umbrella sampling. When I execute:
*mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
The gro file generated at the end shows the ligand is way far compared to
starting position, as if another pulling is done !
Please suggest me a way to tackle this issue. If this thing happens to all
the configurations generated during pulling then how am I supposed to get
the PMF ?

The md_umbrella.mdp I'm using is:
title       = Umbrella pulling simulation
define      = -DPOSRES
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 5000000   ; 10 ns
nstcomm     = 10
; Output parameters
nstxout     = 50000     ; every 100 ps
nstvout     = 50000
nstfout     = 5000
nstxtcout   = 5000 ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes
; 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     = Protein   Non-Protein
tau_t       = 0.5 0.5
ref_t       = 310 310
; 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                    = umbrella
pull_ngroups            = 1
pull_group0             = Protein_chain_A
pull_group1             = ACO
pull_geometry           = direction
pull_dim                = N N Y         ; pulling in Z dimension
pull_rate1              = 0.0
pull_k1                 = 1000           ; kJ mol^-1 nm^-2
pull_start              = yes           ; define initial COM distance > 0
pull_vec1               = 0 0 -1

My question is despite the pull_rate1 being 0.0, why the ligand is moving ?
Is it the pull_start or something else I'm missing here resulting in such a
crash ?

Your suggestions will be highly appreciated.
Thank you.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*