Yes, that's right.
Sorry for my obstinate choice of kcal/mol. Historical/lab reasons. I
should put a disclaimer on the page.
David
On 5/24/07, Jeroen van Bemmelen <[EMAIL PROTECTED]> wrote:
Robert,
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.
Jeroen
> Date: Thu, 24 May 2007 13:59:58 -0400
> From: "Robert fiske" <[EMAIL PROTECTED]>
> Subject: [gmx-users] free energy tutorial results
> To: gmx-users@gromacs.org
> Message-ID: <[EMAIL PROTECTED]>
> 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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