[gmx-users] dg/dl at lambda = 1
dmobley at gmail.com
Wed Oct 18 18:01:38 CEST 2006
> Dear gromacs users,
> I am trying to use FEP method for the calculation of relative binding free
> energy of peptide-protein complex. I am using gmx-3.3.1.
> As per previous discussions on the mailing list, i learnt that i need to
> do two different sets of simulations for my case. first set will be for
> modification of electrostatics and second one for vdw. The second set
> should be started with a structure from the last simulation of first set.
> And every simulation in each set should be run independent of each other
> with em and water-equilibration at each lambda value.
> following are the values for peptide only (not in complex) simulation in
> SPC216 water-box...
> lambda dg/dl (avg) error
> 0.0 55.777174 0.586923
> 0.015 57.524631 0.808737
> 0.03 54.648669 1.03151
> 0.05 54.833890 1.08532
> 0.1 52.990600 1.70822
> 0.2 50.377182 1.74758
> 0.35 46.725657 0.683906
> 0.5 37.016530 0.826907
> 0.65 33.239827 2.03776
> 0.75 27.867797 0.300761
> 0.85 15.989920 1.66024
> 0.9 1.591218 0.924152
> 0.95 -32.877432 1.58611
> 0.99 -259.656906 9.28882
I assume this is for a calculation where you're inserting/deleting one
or more particles? Are you using soft core? This sort of behavior is
typical when you're doing insertion/deletion without soft core (I
would expect the problem to be near lambda=1 if you are doing deletion
without soft core).
You can of course also have similar problems if you are using soft
core but are using non-ideal parameters for soft core (i.e. the soft
core parameters listed in my tutorial are very carefully chosen).
> error is calculated by using g_analyze with -ee option
> i am getting very huge values at lambda = 1.0. as can be seen from the
> values, the steepness of the graph has increased a lot towards end. for
> l=1, dg/dl values go till ~ -2 x 10^11.
> what can be wrong? I have used the same version of gmx for the
> tutorial provided by Dill group. In that case, i am not getting any
> I am completely clueless here... please help..
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