[gmx-users] Implementing Hamiltonian replica exchange simulations
Michael Shirts
mrshirts at gmail.com
Tue Oct 15 17:23:53 CEST 2019
Hamilton replica exchange is implemented in GROMACS (unless it's been
broken in some way). See
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
for
an older tutorial, but it should be relatively straightforward to adjust to
current call patterns.
On Tue, Oct 15, 2019 at 8:18 AM Searle Duay <searle.duay at uconn.edu> wrote:
> 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
> --
> Gromacs Users mailing list
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