Rebeca García Fandiño wrote:
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".
Oops, that should have read "you will *need* lots of well-converged data."
Do you mean I will need also more windows besides extending the simulations?
I doubt you need more windows. Likely you just need more time in each.
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...
Interactions are part of the dissociation process and are not problematic per
se. But if you're trying to obtain only a one-dimensional PMF then your
rotation could be a problem. Is there some reason you need a one-dimensional
PMF and not a three-dimensional PMF? What are you trying to achieve?
-Justin
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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--
========================================
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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