[gmx-users] NPT-REMD

[Michael Shirts]

Pressure should fluctuate significantly.  The estimator for the
pressure that is generally used is very noisy. The question is, do the
pressure averages over, say, 500 ps or 1 ns look about right?

On Sun, Aug 25, 2013 at 5:07 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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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