[gmx-users] Implementing Hamiltonian replica exchange simulations
Matthew Fisher
matthew.fisher at stcatz.ox.ac.uk
Tue Oct 15 14:43:57 CEST 2019
It's possible to implement HREX-MD with the Plumed patch. A tutorial for it is here - https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html
If you're interested in the scientific basis behind the methodology then take a look here
https://www.tandfonline.com/doi/full/10.1080/00268976.2013.824126
Best,
Matthew
Matthew Fisher
DPhil Candidate in Inorganic Chemistry (L.L.Wong Group)
Inorganic Chemistry Laboratory
South Parks Road
Oxford
OX1 3QR
UNITED KINGDOM
Tel (Office): +44 (0)1865 272679
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Searle Duay <searle.duay at uconn.edu>
Sent: 15 October 2019 12:02
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Implementing Hamiltonian replica exchange simulations
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
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