[AMBER] Sander QMMM Bomb Problem

From: Gulsevin,Alican <agulsevin.ufl.edu>
Date: Thu, 14 May 2015 15:56:59 -0400

I posted this a while ago, but since no one replied since then, I am


I am trying to do umbrella sampling on a system of two water molecules
and a small ligand of ~20 atoms in an octahedral water box. I use
scc-dftb for the qm part and the only mm atoms are TIP3P waters.
However, my calculations crash after some time, giving the good old
"sander qmmm bomb error". Now, I am aware this is happening because my
molecule drifts away to the edges of the water box to a distance less
than the qm cutoff defined. Since my system is so small, drifting in
solvent is inevitable. I tried increasing the solvent box up to 24A and
increasing the box size postpones the bitter end, but having to add so
many water molecules for a QM system of 25 atoms is crippling. My
question is, is there a way I can recenter the water box around the
ligand after a certain number of steps. Or else, what could you suggest
to overcome this problem?


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Received on Tue May 19 2015 - 09:00:03 PDT
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