[gmx-developers] Re: REMD and network.c

[alberto]

For now I was just using one cpu per replica to understand what was happening:

mpirun  -np $NSLOTS -machinefile $TMPDIR/machines
/netapp/home/alberto/opteron/gromacs-git/src/kernel/mdrun -s cpeptide_md_.tpr
-multi $NSLOTS -replex 1000 -o 1ctf.trr >& err

The input for _0.mdp was:
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000     ; total 5 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl                   = v-rescale
; Groups to couple separately
tc-grps                  = system
; Time constant (ps) and reference temperature (K)
tau-t                    = 2.0
ref-t                    = 300
; Random seed for Andersen thermostat
andersen_seed            = -1
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

Thanks,
Alberto