On 5/7/17 2:22 PM, abhisek Mondal wrote:
Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.
You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't move this
way.
If you set pull_k1 to zero, it won't accomplish anything at all. You'll have no
biasing force.
You mentioned that during this run we want to restrain the ligand or don't
want to change the configuration generated by pulling simulation.
Is this approach right?
I don't understand the second question.
-Justin
On May 7, 2017 11:37 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:
On 5/7/17 1:57 AM, abhisek Mondal wrote:
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.
Your setup is incorrect. You're applying a biasing potential only along z,
so the ligand can move freely along x and y. A protein-ligand complex has
spherical symmetry, so you should set the reaction coordinate to the vector
connecting the ligand with some suitable subset of interacting protein
residues. You're following the tutorial too literally and that's not
correct. Also do not restrain the protein (I say this weekly; not enough
people are reading the details of the tutorial and associated paper and
just copying .mdp settings...)
-Justin
On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal <abhisek.m...@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*
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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