[gmx-users] NPT-REMD

[rahul seth]

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.


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.