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Martin Kurečka
Plumed AlphaFold
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5f49c998
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5f49c998
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8 years ago
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Giovanni Bussi
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Updated hrex tutorial
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user-doc/tutorials/hrex.txt
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@@ -122,13 +122,22 @@ Notice that total cell could be charged. This happens whenever the scaled portio
is not neutral. There should be no problem in this. When used with pbc, GROMACS
will add a compensating background.
Suggested check
s
:
Suggested check:
- Try with several identical force fields (hardcode the same lambda for all replicas in the
script above) and different seed/starting point. Acceptance should be 1.0
Notice that when you run with GPUs acceptance could be different from 1.0.
The reason is that to compute the acceptance GROMACS is sending the coordinates to the neighboring
replicas which then recompute energy. If all the tpr files are identical, one would expect
energy to be identically to the originally computed one. However, calculations
made with GPUs are typically not reproducible to machine precision. For a large system, even
an error in the total energy for the last significant digit could be on the order of a kJ.
This results in practice in a lower acceptance. The error induced on the final ensemble is
expected to be very small.
Warnings:
- Topologies should have the same number of atoms, same masses and same constraint topology
- Acceptance is not computed correctly if rcoulomb!=rvdw.
- Choose neighbor list update (nstlist) that divides replex. Notice that running with GPUs
GROMACS is going to change nstlist automatically, be sure that it still divides replex.
- Option -hrex requires also option -plumed. If you do not care about plumed, just provide an empty
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