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Martin Kurečka
Plumed AlphaFold
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38f9b8e9
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38f9b8e9
authored
5 years ago
by
Giovanni Bussi
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Fix #410 - DOC ONLY
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user-doc/tutorials/hrex.txt
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@@ -129,7 +129,7 @@ do
# -maxwarn is often needed because box could be charged
grompp_mpi_d -maxwarn 1 -o topol$i.tpr -f grompp$i.mdp -p topol$i.top
done
mpirun -np $nrep gmx_mpi mdrun_d -v -plumed plumed.dat -multi $nrep -replex 100 -nsteps 15000000 -hrex
mpirun -np $nrep gmx_mpi mdrun_d -v -plumed plumed.dat -multi $nrep -replex 100 -nsteps 15000000 -hrex
-dlb no
\endverbatim
Notice that total cell could be charged. This happens whenever the scaled portion of the system
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@@ -156,6 +156,9 @@ Warnings:
unnoticed errors in the final results.
- 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.
- It seems that when using multiple processes per replica it is necessary to switch off
dynamic load balancing (`-dlb no`) otherwise the simulation could crash randomly,
see \issue{410}.
- Option -hrex requires also option -plumed. If you do not care about plumed, just provide an empty
plumed.dat file.
- It should work correctly if replicas have different force-field, temperature, lambda, pressure,
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