Dear admins,
I am following the tutorial "
http://ambermd.org/tutorials/advanced/tutorial6/section2.htm"
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
charges).
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,
Emanuele
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Received on Fri Jul 27 2018 - 09:00:02 PDT
