On 6/27/12 7:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proceed my pulling :
grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
mdrun -s pull.tpr -deffnm pull
title = Umbrella pulling simulation
define = -DPOSRES
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 500000 ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 0
nstvout = 0
nstfout = 500
nstxtcout = 1000 ; every 1 ps
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 = 1.2
vdwtype = Switch
rvdw-switch = 1.0
; 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
; Temperature coupling is on
tcoupl = V-rescale ; modified
Berendsen thermostat
tc_grps = Protein LIG_Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 298 298 ; reference
temperature, one for each group, in K
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
; 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_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = LIG
pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns
pull_k1 = 500 ; kJ mol^-1 nm^-2
I run 3 pulling simulations with the same mdp and I obtain 3
different profiles (Force vs time). Then I used 2xlonger pulling with
the same pulling distance and I run 3 simulations again. Each time I
obtain different profile. Can anyone explain me this? I am using
velocities from npt simulation as above (gen_vel = no and continuation
= yes) so I presume the output should be similar. Please, advice.
I assume you're passing a checkpoint file to grompp? If you're relying on
velocities from the .gro file, they are of insufficient precision to guarantee
proper continuation.
Small variations are inherent in any simulation set, and in the case of pulling,
small changes (though intentional) are the basis for Jarzynski's method. In any
case, all MD simulations are chaotic and so it depends on what your definition
of "different" is in the context of whether or not there are meaningful changes
imparted through the course of each simulation. Also note that in the absence
of the -reprod flag, the same .tpr file may result in a slightly different
outcome. The implications of these outcomes are limited by sampling; the
ensemble should converge with sufficient time and/or replicates. For
non-equilibrium processes like pulling, convergence is probably harder, but
again you have to ask whether the differences are meaningful.
http://www.gromacs.org/Documentation/Terminology/Reproducibility
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
