[gmx-users] dg/dl at lambda = 1

[David Mobley]

Hi,

> 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).

David

> 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
> problem....
>
> I am completely clueless here... please help..
>
> thanks
> bharat
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