[gmx-users] Implementing Hamiltonian replica exchange simulations

[Searle Duay]

Thank you Prof. Lemkul. I haven't seen any discussion either on doing HREX.

-Searle

On Tue, Oct 15, 2019 at 5:18 AM Justin Lemkul <jalemkul at vt.edu> wrote:

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