[gmx-users] large error bars in PMF

Rebeca García Fandiño regafan at hotmail.com
Thu Jul 21 20:07:37 CEST 2011

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,

From: regafan at hotmail.com
To: gmx-users at gromacs.org
Date: Thu, 21 Jul 2011 16:36:59 +0000
Subject: [gmx-users] large error bars in PMF

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


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