[gmx-users] Re: density vs time?

[xianghong qi]

sure, here it is :
**************************************
; 50ns NVT production
integrator               = sd
ld_seed                  = -1
; start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 25000000
; 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                  = 25000000
nstvout                  = 25000000
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 500 ; every 1 ps
nstenergy                = 50000 ; every 100 ps
; Output frequency and precision for xtc file
nstxtcout                = 50000 ; every 100 ps
xtc-precision            = 10000
xtc_grps                 = system
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz or none
pbc                      = xyz
; nblist cut-off
rlist                    = 1.0
domain-decomposition     = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = pme
;rcoulomb-switch          = 0
rcoulomb                 = 1.0
; 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                     = 0.9
rvdw-switch              = 0.8
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = EnerPres
; OPTIONS FOR TEMPERATURE COUPLING
tc_grps                  = system
tau_t                    = 1.0  ; Langevin friction constant (ps)
ref_t                    = 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl                   = No
pcoupltype               = isotropic
tau_p                    = 5.0
compressibility          = 4.5e-05
ref_p                    = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
; OPTIONS FOR BONDS
constraints              = hbonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
unconstrained-start      = yes
*******************************************



On Wed, Nov 5, 2008 at 4:22 PM, Ángel Piñeiro <angel.pineiro at usc.es> wrote:

>  Are you working at constant volume? It would be useful to see your mdp
> file…
>
>
>
> Angel.
>
>
>
>
>
> *De:* gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> *En nombre de *xianghong qi
> *Enviado el:* miércoles, 05 de noviembre de 2008 10:18 p.m.
> *Para:* Discussion list for GROMACS users
> *Asunto:* [gmx-users] Re: density vs time?
>
>
>
> Hello, all:
>
> I checked the mailing list. Looks like g_energy can calculate density vs
> time, but
> my g_energy doesn't have options like density, volume?  I am wondering how
> I can
> get my density vs time graph?  Any suggestion is appreciated. Thanks.
>
> -Xianghong Qi
>
>
>
> --
> Some people make the world more special just by being in it.
>
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-- 
Some people make the world more special just by being in it.
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