Rebeca García Fandiño wrote:
Hi,
I am trying to calculate the binding energy of two molecules using the
PMF (Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of
windows used in the Umbrella Sampling calculations different results
were obtained, and I was suggested to extend my simulations since the
error bars associated to each windows were too high.
I have now extended my simulations from 1 ns to 8 ns, however, I cannot
see much different from the shorter calculations. I send you the
comparison of the two PMF including the error bars (attached).
Now I am using 50 windows, but the shorter simulations were done using
100 windows, so I don't think increasing the number of windows could help.
My system has about 29200 atoms (where 29000 are chloroform atoms). The
*mdp file I am using is copied below.
Would you have any suggestion to improve the results and decrease the
error bars in the calculations?
Neither of the PMF profiles look converged. In the case of 8-ns sampling, you
do not have a well-defined energy minimum and the whole plot is very rough.
This suggests to me that you still need more sampling time. Keep in mind that
even 8 ns is a very tiny amount of sampling in each window.
What is it that you're trying to pull? What are r_1 and r_2? Are they
components of a small peptide or something else? It looks as if the total DG is
going to be somewhere on the order of 6 kcal/mol, so if you want reasonable
error bars you will not lots of well-converged data.
-Justin
----------------------------MDP file---------------------------
title = Umbrella pulling simulation
define =
define =
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 500000 ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
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 = ACH CL3
tau_t = 0.5 0.5
ref_t = 300 300
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 1.0
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
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
-----------------------------------------------
Thanks a lot in advance.
Best wishes,
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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