[gmx-users] problem in NPT equilibration

[Justin Lemkul]

On 11/5/14 6:40 AM, soumadwip ghosh wrote:
> Hello,
>          I have been trying to simulate a double stranded DNA in water in
> presence of ions having hydrophobic sites. What I am doing after energy
> minimization is to elevate the temperature of the system to 300 K in 100 ps
> in the NPT ensemble and after that I am equilibriating the system under NPT
> conditions for 10 ns. But I am not getting the pressure fixed at 1 bar when
> I am checking it. The details of my NPT.mdp file and the outcomes are given
> below.
>
> Kindly help me.
>
> Thanks and regards,
> Soumadwip
>
> title           = OPLS Lysozyme NPT equilibration
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 5000000               ; 2 * 500000 = 1000 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 0             ; save coordinates every 0.2 ps
> nstvout         = 0             ; save velocities every 0.2 ps
> nstenergy       = 0             ; save energies every 0.2 ps
> nstlog          = 1000          ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = yes           ; Restarting after NVT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1             ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1             ; short-range electrostatic cutoff (in nm)
> rvdw            = 1             ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = DNA   SOL     ION     ; three coupling groups - more
> accurate
> tau_t           = 0.1   0.1     0.1     ; time constant, in ps
> ref_t           = 300   300     300     ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl          = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 2.0           ; time constant, in ps
> ref_p           = 1.0           ; reference pressure, in bar
> compressibility = 4.5e-5        ; isothermal compressibility of water,
> bar^-1
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; Velocity generation is off
> ~
> ~
>
> I am getting 37 bar pressure with RMSD, total drift and err estimate all
> zero.
>

You have nstenergy = 0 in the .mdp file, so I wouldn't trust anything that comes 
out of energy analysis.

Also, do not couple solvent and ions separately; it's not generally stable or 
sensible.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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