[gmx-users] free energy tutorial results

Jeroen van Bemmelen J.J.M.vanBemmelen at tnw.tudelft.nl
Thu May 24 23:42:27 CEST 2007


Please check your units: GROMACS uses kJ/mol, while the tutorial uses 
kcal/mol, if I remember correctly. So there's a factor 4.2 between 
those two.


> Date: Thu, 24 May 2007 13:59:58 -0400
> From: "Robert fiske" <rfiske_ at hotmail.com>
> Subject: [gmx-users] free energy tutorial results
> To: gmx-users at gromacs.org
> Message-ID: <BAY118-F326F4F445CBD973E23896190340 at phx.gbl>
> Content-Type: text/plain; format=flowed
> I am trying to follow the free energy tutorial by David. Mobley, however my 
> results are quite a bit off (after integration I get around -9.07) I have 
> only used lambda's spaced at 0,0.1,0.2,... but surely I should be much 
> closer than to the printed values of -2.18+/-0.01.  I am unsure if I am 
> making my mistake on the actual running of the free energy calculations 
> (since I've just copied and pasted my mdp files from the printed tutorial I 
> shouldn't have been able to screw that part up too much I would hope), the 
> only change I made was to set rlist and rcoulomb equal.  Or If I am messing 
> up in the data analysis part.  So this brings me to my question:
> Does anyone who has successfully run this tutorial have their dgdl.xvg files 
> from the individual runs (or the output from g_energy) so that I can see if 
> my simulations are correct, totally wrong, or if only a few lambda values 
> are off.
> Thank you for any assistance you can provide
> Robert Fiske
> Gogonea Group
> Cleveland Statue University

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