diff --git a/user-doc/tutorials/aa-lugano-2.txt b/user-doc/tutorials/aa-lugano-2.txt index a934354a5e85911795f2356cf7264632ec5e7209..7ed10f7d2f18c318253c9f167c44852c22515160 100644 --- a/user-doc/tutorials/aa-lugano-2.txt +++ b/user-doc/tutorials/aa-lugano-2.txt @@ -278,10 +278,45 @@ In the next exercise we will perform a WHAM Umbrella Sampling simulation. \section lugano-2-ex-4 Exercise 4: WHAM Umbrella Sampling - +In this case we will run many simulations with a strong harmonic restraint centered around specific values of phi in such a way to cover all possible values, keep each simulation +close to its specific value, allow for overlap between neighbour simulations, i.e. simulations centered aroud consecutive phi values. The simulation can be either performed in parallel +by preparing starting configurations close to each value or sequentially, extracting a good starting conformation from the former simulations. In the specific case of alanine dipeptide +we can even just start always from the same configuration and let the bias quickly move it close to the target values. +To run the simulation in scalar you can make use of the provided bash script that is: + +\verbatim +for AT in -3.00 -2.75 -2.50 -2.25 -2.00 -1.75 -1.50 -1.25 -1.00 -0.75 -0.50 -0.25 0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25 2.50 2.75 3.00 +do + +cat >plumed.dat << EOF +# vim:ft=plumed +MOLINFO STRUCTURE=diala.pdb +phi: TORSION ATOMS=@phi-2 +psi: TORSION ATOMS=@psi-2 +# +# Impose an umbrella potential on CV 1 +# with a spring constant of 250 kjoule/mol +# at fixed points along phi +# +restraint-phi: RESTRAINT ARG=phi KAPPA=250.0 AT=$AT +# monitor the two variables and the bias potential from the two restraints +PRINT STRIDE=10 ARG=phi,psi,restraint-phi.bias FILE=COLVAR$AT +EOF + +gmx mdrun -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc -nb cpu + +done +\endverbatim + +you can run it using + +\verbatim +./run_us.sh */ +Plotting the phi collective variable for all replica you will see that each simulation has explored a well defined region of the conformation space as defined by phi. + link: @subpage lugano-2 description: This tutorial explains how to use PLUMED to run simple restrained simulations and account for the bias in the analysis diff --git a/user-doc/tutorials/lugano-2/run_us.sh b/user-doc/tutorials/lugano-2/run_us.sh new file mode 100755 index 0000000000000000000000000000000000000000..a7016583de844a00b9f4fc900f2f2930f573c546 --- /dev/null +++ b/user-doc/tutorials/lugano-2/run_us.sh @@ -0,0 +1,21 @@ +for AT in -3.00 -2.75 -2.50 -2.25 -2.00 -1.75 -1.50 -1.25 -1.00 -0.75 -0.50 -0.25 +0.00 +0.25 +0.50 +0.75 +1.00 +1.25 +1.50 +1.75 +2.00 +2.25 +2.50 +2.75 3.00 +do + +cat >plumed.dat << EOF +# vim:ft=plumed +MOLINFO STRUCTURE=diala.pdb +phi: TORSION ATOMS=@phi-2 +psi: TORSION ATOMS=@psi-2 +# +# Impose an umbrella potential on CV 1 and CV 2 +# with a spring constant of 500 kjoule/mol +# at fixed points on the Ramachandran plot +# +restraint-phi: RESTRAINT ARG=phi KAPPA=250.0 AT=$AT +# monitor the two variables and the bias potential from the two restraints +PRINT STRIDE=10 ARG=phi,psi,restraint-phi.bias FILE=COLVAR$AT +EOF + +gmx_mpi mdrun -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc -nb cpu + +done