[gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Hi,

For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Is this normal given that the mdp code being used ? I basically have no
idea with this step, so please help me out. I'm using gromacs-4.6.2.


On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal <abhisek.mndl at gmail.com>
wrote:

> 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*
>



-- 
Abhisek Mondal

*Senior Research Fellow*

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

*Kolkata 700032*

*INDIA*