[AMBER] Thermodyncamic Integration (TI)

From: emanuele falbo <falbo.emanuele.gmail.com>
Date: Fri, 27 Jul 2018 16:45:14 +0100

Dear admins,

I am following the tutorial "
 to calculate the free energy for the simple reaction

Ox + e- → Red

by means of the TI method. Amber works well (only in serial) when the
solvent is not implemented explicitly. However, when I include the solvent
and ions in the systems sander doesn't work- I noticed it's because the
final and initial structure must have the same coordinates.

So my questions are :

1. How do I include the solvent in the two structure keeping the
coordinates of the two systems equal? (Ox and Red differ only for the

2. Why doesn't SANDER work in parallel? ( I followed exactly the
instructions in the tutorial , and also it sound weird cause I am able to
run sander.MPI for simple Molecular Dynamics)

Any advice is really appreciated.

Best Regards,
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Received on Fri Jul 27 2018 - 09:00:02 PDT
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