[gmx-users] Implementing Hamiltonian replica exchange simulations

[Searle Duay]

Hi everyone,

I want to do Hamiltonian replica exchange simulations on my helical peptide
transitioning from transmembrane state to surface-bound state. My
collective variable is the angle between the z-axis and the peptide helical
axis. I have 30 windows with different initial configurations. Here is an
example of mdp file for a window:

integrator              = md
dt                      = 0.002
nsteps                  = 50000000
nstlog                  = 500000
nstxout                 = 1000
nstvout                 = 1000
nstfout                 = 1000
nstcalcenergy           = 100
nstenergy               = 1000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
tcoupl                  = Nose-Hoover
tc_grps                 = PROT   MEMB   SOL_ION
tau_t                   = 1.0    1.0    1.0
ref_t                   = 300 300 300
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0
compressibility         = 4.5e-5  4.5e-5
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = PROT   MEMB   SOL_ION
;
refcoord_scaling        = com
;
pull                    = yes
pull_ncoords            = 1
pull_ngroups            = 2
pull-group1-name        = n_com
pull-group2-name        = c_com
pull-coord1-type        = umbrella
pull-coord1-geometry    = angle-axis
pull-coord1-groups      = 1 2
pull-coord1-vec         = 0 0 -1
pull-coord1-start       = no
pull-coord1-init        = 3.0
pull-coord1-k           = 1000.0

The mdp file for each window varies only in the pull-coord1-init parameter
(ranging from 3 to 90 degrees, in 3-degree intervals). Then, I grompp to
get 30 different tpr files.

This is the command that I use for running the simulations:

srun --mpi=pmi2 gmx_mpi mdrun -s window.tpr -replex 1000 -multidir angle0
angle1 angle2 angle3 angle4 angle5 angle6 angle7 angle8 angle9 angle10
angle11 angle12 angle13 angle14 angle15 angle16 angle17 angle18 angle19
angle20 angle21 angle22 angle23 angle24 angle25 angle26 angle27 angle28
angle29 -maxh 119.5

And I'm getting the following error:
The properties of the 30 systems are all the same, there is nothing to
exchange

I'm wondering where the error comes from. My systems should be different
such that the target angle is different in each window. I'm not sure if I
am giving the correct input to GROMACS.

Thanks for your help,
Searle

-- 
Searle Aichelle S. Duay
Ph.D. Student
Chemistry Department, University of Connecticut
searle.duay at uconn.edu