[gmx-users] request for comments on profile.xvg (PMF) courve

Przemek Bartha przemekbartha at gmail.com
Mon Nov 7 17:55:10 CET 2011

Dear gmx users,
my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of which one is pulled from the other. I followed Justin's tutorial on umbrella sampling.
Here are the results.

I would be grateful, if anyone could tell me why is the PMF so irregular, unstable, unlike the courve in the tutorial:

After a little bit of research on "gmx-users", my guess is either incorrent sampling or/and some major mistake in parametrization.
I tried to resample the simulation so that the "umbrellas" don't overlap as much as they do in my histo.xvg file but it changed the PMF totaly and did not resolve the problem.
Or maybe, it is just the way it should be?

My pullcode is nearly the same as in the tutorial. I don't want to trash, but if you require any additional information, please let me know.
The sampling is twice as small as in the tutorial since my computational resources are limited, but when I tried running more precise sampling, the results were pretty much the same (irregular courve).

Thanks in advance.

part of md_umbrella.mdp:

; Run parameters
integrator = md
dt = 0.004
tinit = 0
nsteps = 2500000 ; 10 ns 
; Pull code 
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes 
pull_ngroups = 1
pull_group0 = Chain_B 
pull_group1 = Chain_A 
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
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