[GaMD-discuss] PPI-GaMD igamd=17 potential statistics = 0

[Irene M. <ire...@ut...>]

Hello everyone,

I am running PPI-GaMD on a protein-oligonucleotide complex.
First of all, although PPI-GaMD has been developed for PPIs, can it be applied also on the kind of complex I am simulating? I am observing unbinding/binding events of the oligonucleotide, but I would like to know your opinion about the suitability of GaMD for these systems.
I am running my simulations with Amber by setting igamd=17, with therefore a dual boost. However, when I give a look at the log files I have the statistics for VmaxD, VminD, VavgD, sigmaVD, but all the statistics for the VmaxP, VminP, VavgP and sigmaVP are 0. Is this normal?
In addition, for the choice of the sigma0 values, I let them to 6 kcal/mol and I verified that the k0 reached 1, but I observe a large sigmaVD. What should I do in this case?

Thanks and best regards
Irene
---------------------------------------------------------------------
Irene Maffucci, PhD
Lab. de Génie Enzymatique et Cellulaire UMR 7025 
Université de technologie de Compiègne
Centre de Recherche Royallieu
CS60319
60203 Compiègne cedex
Tel. +33 (0)3 44 23 43 42