[gmx-users] Implementing Hamiltonian replica exchange simulations

[Justin Lemkul]

On 10/14/19 3:48 PM, Searle Duay wrote:
> 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.

There is no topological difference in your systems and the Hamiltonians 
are all the same, so mdrun won't perform any kind of exchange between 
the different simulations. The manual says HREX is supported but I have 
never seen much discussion on how to make it work. It will be a 
lambda-dependent process, however, since that's the only way to alter 
the Hamiltonian of each subsystem.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================