On 14/06/2012 3:56 PM, Tom Dupree wrote:
Greetings all,
I can't manually reproduce g_lie results.
After raging at excel for a while I think I have found a bug.
Here is my first time point,
Reported by g_lie to be 35.0073
> From energy file
Lj_complex =-130.762
Coul_complex = -286.746
My constants specified to g_lie
Clj = Alpha = lj_const = 0.181
Cqq = Beta = coul_const = 0.43
Elj = Lj_solv = -166
Eqq = Coul_solv = -263
Therefore
Lj_diff = 35.238
Coul_diff = -23.746
Hence
Lj_diff x lj_const = 6.378
Coul_diff x coul_const = -10.211
And there is no way I can add those to get 35.0073
However I can get this value using the following
Coul_complex - lj_solv = -120.746
Lj_complex - coul_solv = 132.2378
-120.746 x lj_const = -120.746 x 0.181 = -21.855
132.2378 x coul_const = 56.86225
Sum = 35.00726
In short I think the g_lie calculation has swapped its variables, Elj instead
of Eqq and vice versa.
I think it's rather more likely you've made a transcription error going
to Excel. You can check the code of src/tools/gmx_lie.c for exactly this
kind of purpose, but I can't see any problem with it.
One other thing I have noticed is that when calculating the average g_lie uses
the final value twice, is there a reason for this?
e.g.
994 24.9397
996 43.3382
998 40.5714
1000 40.5585
1000 40.5585
Inspect your energy file with gmxdump - I think you've managed to
duplicate the final frame at an earlier point of your workflow. eneconv
has options to prevent such duplicates occuring during concatenation,
etc. In any case, g_lie just eats what you give it...
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
