Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1 and r_2).
I did not understand very well your last suggestion: "...if you want reasonable
error bars you will not lots of well-converged data".
Do you mean I will need also more windows besides extending the simulations?
I think the problem could be also that the peptides I am using rotate in the
box and they do not remain flat one respect to the other. They gyrate freely
and some parts of their structure interact along the pulling...
Thanks a lot again for your help.
Best wishes,
Rebeca.
From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Thu, 21 Jul 2011 16:36:59 +0000
Subject: [gmx-users] large error bars in PMF
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?
----------------------------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
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