tutorials update to reflect the new

gromacs syntax (gmx_mpi mdrun) instead of (mdrun_mpi)

user-doc/tutorials/belfast-4.txt

@@ -209,7 +209,7 @@ The <a href="tutorial-resources/belfast-4.tar.gz" download="belfast-4.tar.gz">ta
 By working in the directory where the topol.tpr file is stored, one can launch gromacs
 with the command
 \verbatim
-mdrun_mpi -plumed plumed.dat -nsteps 100000
+gmx_mpi mdrun -plumed plumed.dat -nsteps 100000
 \endverbatim
 (notice that the -nsteps flag allows the number of steps to be changed).
 
@@ -409,7 +409,7 @@ restraint-phi: RESTRAINT ARG=phi KAPPA=40.0 AT=$AT
 PRINT STRIDE=10 ARG=phi,psi,restraint-phi.bias FILE=COLVAR$AT
 EOF
 
-mdrun_mpi -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc
+gmx_mpi mdrun -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc
 
 done
 

user-doc/tutorials/belfast-6.txt

@@ -135,7 +135,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -plumed
+gmx_mpi mdrun -plumed
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.

user-doc/tutorials/belfast-7.txt

@@ -119,7 +119,7 @@ PRINT STRIDE=10 ARG=phi,psi FILE=COLVAR
 To submit this simulation with Gromacs, we need the following command line.
 
 \verbatim
-mpirun -np 2 mdrun_mpi -s TOPO/topol -plumed -multi 2 -replex 100
+mpirun -np 2 gmx_mpi mdrun -s TOPO/topol -plumed -multi 2 -replex 100
 \endverbatim
 
 This command will execute two MPI processess in parallel, using the topology files
@@ -198,11 +198,11 @@ For the analysis of the demuxed trajectories, we can use the -rerun option of Gr
 
 \verbatim
 # rerun Gromacs on replica 0 trajectory
-mdrun_mpi -s TOPO/topol0.tpr -plumed plumed_demux.dat -rerun 0_trajout.xtc
+gmx_mpi mdrun -s TOPO/topol0.tpr -plumed plumed_demux.dat -rerun 0_trajout.xtc
 # rename the output
 mv COLVAR_DEMUX COLVAR_DEMUX.0
 # rerun Gromacs on replica 1 trajectory
-mdrun_mpi -s TOPO/topol1.tpr -plumed plumed_demux.dat -rerun 1_trajout.xtc
+gmx_mpi mdrun -s TOPO/topol1.tpr -plumed plumed_demux.dat -rerun 1_trajout.xtc
 # rename the output
 mv COLVAR_DEMUX COLVAR_DEMUX.1
 \endverbatim
@@ -236,7 +236,7 @@ of the simulation. We will now use 4 replicas at the following temperatures: 300
 We can use the same PLUMED input file described above (plumed.dat), and execute Gromacs using the following command line:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed -multi 4 -replex 100
 \endverbatim
 
 At the end of the simulation, we first monitor the diffusion in temperature space of each replica.
@@ -320,7 +320,7 @@ PRINT STRIDE=10 ARG=phi,psi,metad.bias FILE=COLVAR
 The PTMetaD simulation is executed in the same way as the PT:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed -multi 4 -replex 100
 \endverbatim
 
 and it will produce one COLVAR and HILLS file per temperature (COLVAR.0, HILLS.0, ...).
@@ -376,7 +376,7 @@ PRINT STRIDE=10 ARG=phi,psi,ene FILE=COLVAR_PT
 As usual, the simulation is run for 400ps using the following command:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed plumed_PT.dat -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed plumed_PT.dat -multi 4 -replex 100
 \endverbatim
 
 At the end of the run, we want to analyze the acceptance rate between exchanges.
@@ -433,7 +433,7 @@ potential energy at 300K, as calculated from the preliminary PT run.
 We run the simulation following the usual procedure:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed plumed_PTWTE.dat -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed plumed_PTWTE.dat -multi 4 -replex 100
 \endverbatim
 
 If we analyze the average acceptance probability in this run:
@@ -512,7 +512,7 @@ parameters and biasfactors in the two metadynamics runs.
 The simulation is carried out using the usual procedure:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed plumed_PTMetaDWTE.dat -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed plumed_PTMetaDWTE.dat -multi 4 -replex 100
 \endverbatim
 
 

user-doc/tutorials/belfast-8.txt

@@ -102,7 +102,7 @@ The four replicas start from the same GROMACS topology file replicated four time
 Finally, GROMACS is launched as a parallel run on 4 cores, with one replica per core, with the command 
 
 \verbatim
-mpirun -np 4 mdrun_mpi -s topol -plumed plumed -multi 4 -replex 2000 >& log &
+mpirun -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4 -replex 2000 >& log &
 \endverbatim
 
 where -replex 2000 indicates that every 2000 molecular-dynamics steps
@@ -315,7 +315,7 @@ PRINT ARG=cv1,cv2,cv3,cv4 STRIDE=1000 FILE=COLVAR
 and the simulation can be run in a similar way without doing exchanges:
 
 \verbatim
-mpirun -np 4 mdrun_mpi -s topol -plumed plumed -multi 4  >& log &
+mpirun -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4  >& log &
 \endverbatim
 
 alternatively Multiple Walkers can be run as independent simulations sharing via the file system the biasing potential,

user-doc/tutorials/belfast-9a.txt

@@ -58,7 +58,7 @@ folder (see first example in the resources tarball), one file for each nucleus.
 This example can be executed as
 
 \verbatim
-mdrun_mpi -s topol -plumed plumed
+gmx_mpi mdrun -s topol -plumed plumed
 \endverbatim
 
 \subsection belfast-9-replica Replica-Averaged Restrained Simulations 
@@ -104,7 +104,7 @@ force field.
 
 This example can be executed as
 \verbatim
-mpiexec -np 4 mdrun_mpi -s topol -plumed plumed -multi 4
+mpiexec -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4
 \endverbatim
 
 The third example show how \ref RDC (calculated with the theta-methods) can be employed in the same way, in this case to describe the native state of Ubiquitin. In 
@@ -128,7 +128,7 @@ In this input the first four N-H RDCs are defined.
  
 This example can be executed as
 \verbatim
-mpiexec -np 8 mdrun_mpi -s topol -plumed plumed -multi 8
+mpiexec -np 8 gmx_mpi mdrun -s topol -plumed plumed -multi 8
 \endverbatim
 
 \section belfast-9-refer Reference

user-doc/tutorials/cambridge.txt

@@ -150,7 +150,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -plumed
+gmx_mpi mdrun -plumed
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
@@ -359,7 +359,7 @@ The, in this case, two replicas start from the same GROMACS topology file replic
 Finally, GROMACS is launched as a parallel run on 4 cores, with one replica per core, with the command 
 
 \verbatim
-mpirun -np 4 mdrun_mpi -s topol -plumed plumed -multi 4 -replex 10000 >& log &
+mpirun -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4 -replex 10000 >& log &
 \endverbatim
 
 where -replex 10000 indicates that every 10000 molecular-dynamics steps exchanges are attempted

user-doc/tutorials/cineca.txt

@@ -91,7 +91,7 @@ that can be modified and used to generate a new .tpr file.
 
 GROMACS can be run (interactively) using the following command:
 \verbatim
-> mdrun_mpi -s ../SETUP/topolA.tpr -nsteps 10000 -x traj.xtc
+> gmx_mpi mdrun -s ../SETUP/topolA.tpr -nsteps 10000 -x traj.xtc
 \endverbatim
 The nsteps flags can be used to change the number of timesteps and topolA.tpr is the name of the tpr file.
 While running, GROMACS will produce a md.log file, with log information, and a traj.xtc file, with a binary trajectory.
@@ -102,7 +102,7 @@ The trajectory can be visualized with VMD using:
 
 To activate PLUMED during a GROMACS MD simulation, you need to add the -plumed flag
 \verbatim
-> mdrun_mpi -s ../SETUP/topolA.tpr -nsteps 10000 -plumed plumed.dat -x traj.xtc
+> gmx_mpi mdrun -s ../SETUP/topolA.tpr -nsteps 10000 -plumed plumed.dat -x traj.xtc
 \endverbatim
 Here plumed.dat is the name of the PLUMED input file. Notice that PLUMED will write
 information in the md.log that could be useful to verify if the simulation has been set up properly.
@@ -345,7 +345,7 @@ Once the PLUMED input file is prepared, one has to run GROMACS with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -s ../SETUP/topolA.tpr -plumed plumed.dat -nsteps 5000000 -x traj.xtc
+gmx_mpi mdrun -s ../SETUP/topolA.tpr -plumed plumed.dat -nsteps 5000000 -x traj.xtc
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
@@ -679,7 +679,7 @@ several simultaneous simulations. This can be done with GROMACS using the
 multi replica framework. That is, if you have 4 tpr files named topol0.tpr,
 topol1.tpr, topol2.tpr, topol3.tpr you can run 4 simultaneous simulations.
 \verbatim
-> mpirun -np 4 mdrun_mpi -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
+> mpirun -np 4 gmx_mpi mdrun -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
 \endverbatim
 Each of the 4 replicas will open a different topol file, and GROMACS will
 take care of adding the replica number before the .tpr suffix.
@@ -805,7 +805,7 @@ done
 And then run GROMACS with the following command: 
 
 \verbatim
-mpirun -np 32 mdrun_mpi -plumed plumed.dat -s topol.tpr -multi 32 -replex 1000 -nsteps 500000 -x traj.xtc
+mpirun -np 32 gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multi 32 -replex 1000 -nsteps 500000 -x traj.xtc
 \endverbatim
 
 To be able to combine data from all the simulations, it is necessary to have an overlap between 

user-doc/tutorials/hrex.txt

@@ -125,7 +125,7 @@ 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 mdrun_mpi_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
 \endverbatim
 
 Notice that total cell could be charged. This happens whenever the scaled portion of the system

user-doc/tutorials/munster.txt

@@ -90,7 +90,7 @@ namely:
 
 Gromacs md can be run using on the command line:
 \verbatim
-> mdrun_mpi -s topolA.tpr -nsteps 10000
+> gmx_mpi mdrun -s topolA.tpr -nsteps 10000
 \endverbatim
 The nsteps flags can be used to change the number of timesteps and topolA.tpr is the name of the tpr file.
 While running, gromacs will produce an md.log file, with log information, and a traj.xtc file, with a binary trajectory.
@@ -101,7 +101,7 @@ The trajectory can be visualized with VMD using a command such as
 
 To run a simulation with gromacs+plumed you just need to add a -plumed flag
 \verbatim
-> mdrun_mpi -s topolA.tpr -nsteps 10000 -plumed plumed.dat
+> gmx_mpi mdrun -s topolA.tpr -nsteps 10000 -plumed plumed.dat
 \endverbatim
 Here plumed.dat is the name of the plumed input file. Notice that PLUMED will write
 information in the md.log that could be useful to verify if the simulation has been set up properly.
@@ -490,7 +490,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
+gmx_mpi mdrun -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
@@ -656,7 +656,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
+gmx_mpi mdrun -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
 \endverbatim
 
 As we did in the previous exercise, we can use COLVAR to visualize the behavior of the CV during the simulation.
@@ -861,7 +861,7 @@ several simultaneous simulations. This can be done with gromacs using the
 multi replica framework. That is, if you have 4 tpr files named topol0.tpr,
 topol1.tpr, topol2.tpr, topol3.tpr you can run 4 simultaneous simulations.
 \verbatim
-> mpirun -np 4 mdrun_mpi -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
+> mpirun -np 4 gmx_mpi mdrun -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
 \endverbatim
 Each of the 4 replicas will open a different topol file, and GROMACS will
 take care of adding the replica number before the .tpr suffix.
@@ -983,7 +983,7 @@ fi
 done
 
 # run REM
-mpirun -np $nrep mdrun_mpi -plumed plumed.dat -s topol.tpr -multi $nrep -replex 1000 -nsteps 500000
+mpirun -np $nrep gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multi $nrep -replex 1000 -nsteps 500000
 \endverbatim
 
 To be able to combine data from all the simulations, it is necessary to have an overlap between