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

[Per Larsson]

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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