[gmx-users] NPT-REMD

[Mark Abraham]

On Sun, Aug 25, 2013 at 6:22 PM, rahul seth
<rahul.seth.gromacs at gmail.com> wrote:
> Hi All,
>
> I have been trying to perform NPT-REMD with a Protein Substrate and water.
> I am trying to use md+nose-hoover thermostat and parrinello-rahman
> barostat. However, I am not quite sure about the tau-t and the tau-p that I
> should be using here. I paste a part of my mdp file below:
> define               =  -DPOSRES_subs
> constraints        =  all-bonds
> pbc                   =  xyz
> integrator           =  md
> ;ld_seed            = %8i
> dt                     =  0.002    ; ps !
> nsteps               =  250000   ; 50 ns
> ;
> nstcomm             =  1
> nstcalcenergy       =  10
> nstxout               =  0
> nstxtcout            =  5000 ;every 10 ps
> nstvout               =  0
> nstfout               =  0
> nstlog                =  1000
> nstenergy           =  1000
> nstlist                =  10
> ns_type             =  grid
> rlist                   =  1.0
> vdwtype             =  cut-off
> rvdw                  =  1.0
> coulombtype         =  pme
> rcoulomb            =  1.0
> fourierspacing      = 0.12
> pme_order           = 4
> ewald_rtol           = 1e-5
> optimize_fft         =  yes
> tcoupl                = nose-hoover
> nsttcouple          = 5
> tc-grps               =  subs Protein SOL
> tau_t                  = 0.2 0.2 0.2
> ref_t                   =  %8.3f %8.3f %8.3f
> ; Energy monitoring
> energygrps          =  subs Protein SOL
> ; Isotropic pressure coupling is now on
> Pcoupl               = parrinello-rahman
> nstpcouple          = 1
> refcoord-scaling   = all
> Pcoupltype          = isotropic
> tau_p                  = 2.0
> compressibility     = 4.5e-5
> ref_p                    = 1.01325
>
>
> Although the temperatures in this case stays close to the desired values,
> the pressures of the individual replicas fluctuate significantly and hence
> I do not think I have weird replica exchange probabilities.

Seemingly large
http://www.gromacs.org/Documentation/Terminology/Pressure fluctuations
are normal - see link. You should satisfy yourself that your .mdp file
produces ensembles that are respectable before you get involved with
REMD, and gathering statistics for that will take longer for pressure
than temperature.

> I have varied tau-t and tau-p from 0.2 to 1 and 1 to 5 respectively. It
> doesn't really seem to improve anything. Can anyone suggest a set of
> optimized values for these parameters? I understand these maybe context
> dependent but to give you a rough idea I have about ~18,000 atoms with 170
> for atoms 1156 for substrate and the rest for water.

Your literature survey of similar simulations should give you an idea
of usage in the field, but (e.g. per GROMACS manual thermostat
section) I would think tau-t for N-H should not go below 1. Otherwise,
first observe whether you have a real problem before making haphazard
changes :-)

Mark

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