[gmx-users] Energy drift

[Xiaobin Cao]

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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