[gmx-users] Box size increases in NPT

[Mark Abraham]

On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" <ndhumal at andrew.cmu.edu> wrote:
>
> Hello,
>
> I am running a NPT simulation for cyclopropylchloride(1) in
> 50%water(100)+50%ethanol(100) using opls force field parameter .
>
> After equilibration box size increases from 20 A to 70 A.

Really? Seems wildly unlikely to have occurred without crashing. Over what
time span? How did you observe before and after? What densities do you
measure?

Mark

> I used the following mdp file.
>
> ; RUN CONTROL PARAMETERS =
> integrator               = sd
> ; start time and timestep in ps =
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 50000
> ; number of steps for center of mass motion removal =
> nstcomm                  = 100
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 500
> nstenergy                = 100
> ; Output frequency and precision for xtc file =
> nstxtcout                = 5000
> xtc-precision            = 1000
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist                  = 10
> ; ns algorithm (simple or grid) =
> ns_type                  = grid
> ;OPTIONS FOR TEMPERATURE COUPLING
> tc_grps                  = system
> tau_t                    = 0.1
> ref_t                    = 290;350
> ;OPTIONS FOR PRESSURE COUPLING
> Pcoupl                   = berendsen
> tau_p                    = 0.5
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> ; OPTIONS FOR BONDS     =
> constraints              = hbonds
> ; Type of constraint algorithm =
> constraint-algorithm     = Lincs
> ; Do not constrain the start configuration =
> unconstrained-start      = no
> ; Relative tolerance of shake =
> shake-tol                = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs-order              = 12
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs-warnangle          = 30
>
> ; Periodic boundary conditions: xyz or none =
> pbc                      = xyz
> ; nblist cut-off         =
> rlist                    = 0.9
> domain-decomposition     = no
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype              = pme
> ;rcoulomb-switch          = 0
> rcoulomb                 = 0.9
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon-r                = 1
> ; Method for doing Van der Waals =
> vdw-type                 = switch
> ; cut-off lengths        =
> rvdw-switch              = 0.8
> rvdw                     = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing           = 0.1
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> ; EWALD/PME/PPPM parameters =
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> optimize_fft             = no
> ; Free energy control stuff
> free_energy              = no
>
>
> Nilesh
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists