[gmx-users] Energy drift

[Mark Abraham]

Hopefully you are following some established protocol for your N2 model. If
so, use its recommendation for time step and or bond constraints. Not using
constraints can lead to your symptoms with 1fs time step - prefer 0.5fs.

Mark


On Tue, Aug 19, 2014 at 9:53 AM, Xiaobin Cao <xcao at lsu.edu> wrote:

> Thank you, David. Please see the below for my mdp file, and the top file
> is also attached. Can you tell me where is my problem?  Thanks
>
>  ;
>  ;513 N2
>  ;
>
>  ; RUN CONTROL PARAMETERS
>  integrator               = md-vv
>  ; start time and timestep in ps
>  tinit                    = 0.0
>  dt                       = 0.001
>  nsteps                   = 5000000
>
>  ; OUTPUT CONTROL OPTIONS
>  ; Output frequency for coords (x), velocities (v)
>  nstxout                  = 50
>  nstvout                  = 50
>  ; Output frequency for energies to log file and energy file
>  nstlog                   = 50
>  nstenergy                = 50
>
>  ; mode for center of mass motion removal
>  comm-mode                = Linear
>  ; number of steps for center of mass motion removal
>  nstcomm                  = 10
>  ; group(s) for center of mass motion removal
>  comm-grps                =
>
>
>  ; OPTIONS FOR BONDS
>  continuation             = yes
>  constraints              = none
>  constraint_algorithm     = Lincs
>  lincs_order              = 4
>  lincs-iter               = 1
>  ; Lincs will write a warning to the stderr if in one step a bond
>
>  ; NEIGHBORSEARCHING PARAMETERS
>  cutoff-scheme            = Verlet
>  nstlist                  = 1
>  ; ns algorithm (simple or grid)
>  rlist                    = 1.8
>  ns_type                  = grid
>  rcoulomb                 = 1.8
>  rvdw                     = 1.8
>  ; Periodic boundary conditions: xyz or no
>  pbc                      = xyz
>
>  ; OPTIONS FOR ELECTROSTATICS AND VDW
>  ; Method for doing electrostatics
>  coulombtype              = cut-off
>  ; Method for doing Van der Waals
>  vdw_type                 = cut-off
>  ; Apply long range dispersion corrections for Energy and Pressure
>  DispCorr                 = Enerpres
>
>
>  ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>  ; Temperature coupling
>  tcoupl                   = nose-hoover
>  ; Groups to couple separately
>  tc_grps                  = System
>  ; frequency for coupling the Temperature
>  nsttcouple               = 1
>  ; Time constant (ps) and reference temperature (K)
>  tau_t                    = 0.4
>  ref_t                    = 298.15
>  ; Pressure coupling
>  Pcoupl                   = no
>  pcoupltype               = isotropic
>  nstpcouple               = 1
>  tau_p                    = 0.4
>  ref_p                    = 1.1
>  compressibility          = 1
>  refcoord_scaling         = com
>
>  ; GENERATE VELOCITIES FOR STARTUP RUN
>  gen_vel                  = no
>  ;gen_temp                 = 293.15
>  ;gen_seed                 = -1
>
>
>
> _____________________________________________
> Xiaobin Cao
> Dept of Geology & Geophysics
> E235, Howe-Russell Geosciences Complex,
> Louisiana State University, Baton Rouge, LA 70803, U.S.A.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van
> der Spoel <spoel at xray.bmc.uu.se>
> Sent: Monday, August 18, 2014 11:51 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Energy drift
>
> On 2014-08-18 22:24, Xiaobin Cao wrote:
> > Dear all,
> >
> >
> >
> > I am looking into transport property in gas phase by GROMACS.
> >
> > For my system (e.g. pure N2 gas), the bond energy and conserved energy
> drift to high linearly with simulation time, while the average pressure
> drifts to low. Does anybody have similar experience or have some ideas on
> it? Is this a bug in GROMACS?
> >
> Depends on your simulation protocol. Gromacs can simulate for
> microseconds without energy drift if the protocol is right.
> >
> >
> > Thanks.
> >
> > _____________________________________________
> > Xiaobin Cao
> > Dept of Geology & Geophysics
> > E235, Howe-Russell Geosciences Complex,
> > Louisiana State University, Baton Rouge, LA 70803, U.S.A.
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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