[gmx-users] [Fwd: PMF or umbrella sampling]

Oliver Beckstein oliver at biop.ox.ac.uk
Fri Dec 9 12:03:31 CET 2005

> Dear all ,
> Someone could give me a correct example of setting PMF in gromacs .
> James
I've got a draft of a tutorial in which you calculate the PMF of an ion  
through a short carbon nanotube, using Gromacs 3.2.1. It's not very  
userfriendly yet (you can call it downright idiosyncratic because its  
geared towards internal use) but you're welcome to act as a alpha  
tester. The input file and the README.txt can be found in one tar file  


Unpack with 'tar -jxvf PMFtutorial-0.1.tar.bz2'.

If you want to actually do all the steps in the tutorial you'll need  
other scripts (see the FILE SOFTWARE.txt in the tar ball).

You will not find a ppa input file in the tar ball because these files  
are generated (that's pretty much the point of the whole exercise) so I  
attached one of the generated files to this email.

I can't promise much help at the moment because I am really snowed in  
with work but perhaps it can get you started; nevertheless, feedback is  
very welcome.

All the best,

; Input for umbrella sampling
; version: Gromacs 3.2.1
; created by prepumbrella.pl, (c) 2004 Oliver Beckstein

verbose   = yes
runtype   = umbrella       ; umbrella sampling
pulldim   = N N Y          ; restrict in Z dimension
reftype   = com         ; compute center of umbrella potential
                            ; relative to initial COM of
reference_group = CNT    ; the reference group

; Umbrella sampling
; group which is subjected to the umbrella potential (see the index  
group_1   = NA_0.325
K1        = 977.37;           ; kJ / (mol nm^2)
Pos1      = 0.000 0.000 0.325  ; centre of the umbrella potential

Oliver Beckstein * oliver at biop.ox.ac.uk

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