[gmx-users] Implementing Hamiltonian replica exchange simulations

Searle Duay searle.duay at uconn.edu
Tue Oct 15 16:18:04 CEST 2019


Hi Matthew,

Thank you very much! I appreciate it.

Best,
Searle

On Tue, Oct 15, 2019 at 8:44 AM Matthew Fisher <
matthew.fisher at stcatz.ox.ac.uk> wrote:

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


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