[gmx-users] Thermostat for REMD simulations in implicit solvent

[César Ávila]

I also noticed this error on my setup, so I changed tau-t to 0.1, which is
commonly found on others setup.
tau-t = 0.0109 seems too low.

2010/11/26 Per Larsson <per.larsson at sbc.su.se>

> Hi!
>
> Have never tried remd with implicit solvent, but note that the unit of
> tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t =
> 0.0109 rather than 91.
>
> Try this and see if the problem goes away!
>
> /Per
>
> 26 nov 2010 kl. 15:55 skrev César Ávila <clavila at gmail.com>:
>
> > Dear all,
> > I am trying to set up a REMD simulation for a peptide (CHARMM ff) in
> implicit solvent (OBC GB).
> > Following Bjelkmar et al* I am using stochastics dynamics integration
> with an inverse friction constant of 91 ps-1, 5 fs timestep,
> > virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff).  The full
> .mdp file is attached at the end of this mail. The problem I am
> > facing is that after a while, the temperatures of all replicas start
> dropping even below the lowest target temperature.
> > Would you suggest changing some parameter or the whole thermostat to
> prevent this from happening?
> >
> > @ s0 legend "Temperature"
> >     0.000000  310.811523
> >     5.000000  435.627045
> >    10.000000  417.161713
> >    15.000000  414.248901
> >    20.000000  399.390686
> >    25.000000  375.087219
> >    30.000000  338.131256
> >    35.000000  339.961151
> >    40.000000  319.424561
> >    45.000000  290.442322
> >    50.000000  289.587921
> >    55.000000  248.746246
> >    60.000000  253.192047
> >    65.000000  242.619476
> >    70.000000  256.051941
> >    75.000000  237.648468
> >    80.000000  231.938690
> >    85.000000  217.029953
> >    90.000000  211.447983
> >    95.000000  210.393890
> >   100.000000  208.518417
> >   105.000000  196.718445
> >   110.000000  219.245682
> >   115.000000  202.957993
> >   120.000000  193.128159
> >   125.000000  198.278198
> >   130.000000  175.304108
> >   135.000000  164.925613
> >   140.000000  195.024490
> >   145.000000  201.153046
> >   150.000000  211.160797
> >   155.000000  189.525085
> >   160.000000  191.156006
> >   165.000000  186.545242
> >   170.000000  186.885422
> >   175.000000  182.838486
> >   180.000000  174.960098
> >   185.000000  175.244049
> >   190.000000  179.517975
> >   195.000000  165.785416
> >   200.000000  189.871048
> >   205.000000  179.510178
> >   210.000000  152.527710
> >   215.000000  160.109955
> >   220.000000  163.564148
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * "Implementation of the CHARMM ff in GROMACS" (2010) JCTC, 6, 459-466
> >
> >
> > ; Run parameters
> > integrator          =  sd
> > dt                  =  0.005    ; ps !
> > nsteps              =  20000
> > nstcomm             = 1
> > comm_mode           = angular       ; non-periodic system
> >
> > ; Bond parameters
> > constraints             = all-bonds
> > constraint_algorithm    = lincs
> > lincs-iter          = 1
> > lincs-order         = 6
> >
> > ; required cutoffs for implicit
> > nstlist             =  0
> > ns_type             =  grid
> > rlist               =  0
> > rcoulomb            =  0
> > rvdw                =  0
> > epsilon_rf          =  0
> > rgbradii            =  0
> >
> > ; cutoffs required for qq and vdw
> > coulombtype         =  cut-off
> > vdwtype             =  cut-off
> >
> > ; temperature coupling
> > tcoupl              = v-rescale
> > tc-grps             = system
> > tau-t               = 91
> > ref-t               = 300
> >
> > ; Pressure coupling is off
> > Pcoupl              = no
> >
> > ; Periodic boundary conditions are off for implicit
> > pbc                 = no
> >
> > ; Settings for implicit solvent
> > implicit_solvent    = GBSA
> > gb_algorithm        = OBC
> > gb_epsilon_solvent  = 78.3
> > sa_surface_tension  = 2.25936
> >
> > ;Output control
> > nstxout             = 1000
> > nstfout             = 0
> > nstvout             = 0
> > nstxtcout           = 0
> > nstlog              = 1000
> > nstcalcenergy       = -1
> > nstenergy           = 1000
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN
> > gen_vel = yes
> > gen_temp = 300
> > gen_seed = 1993
> >
> >
> >
> > --
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