[gmx-users] frustrating NVE

[David]

On Fri, 2005-11-11 at 06:42 +0800, Xiaobing Feng wrote:
> Dear everyone,
>  
>    I did a MD NVE run. The total energy is going up nearly linearly,
> total energy went from -46000 kJ/mol to -45700 kJ/mol after 450 ps, and no sign
> to level off.  There is no close contacts in the conf.gro, and the run is pretty
> long, the system should be equilibrated long ago.  The system is made of a solid
> and its melt, an interfacial system.
>    The main setting is :
>    dt =1fs,  Coulombtype=PME, rlist = rvdw = rcoulomb=1.2, fourierspacing=0.1,
>    pme_order=4, ewald_rtol=1e-5
>    There is one H atom, O-H bond is contrainted by Lincs.
>    Given in the following is the complete mdout.mdp ( I removed comments only). 
>  Could anybody tell me what's wrong with my setting?
You may want to use a shifted Vdw potential, e.g. from 1.0 to 1.2 nm

> 
>   Thanks a lot.
> 
>   Xiaobing
> ---------------mdout.mdp -----------------------   
> 
> 
> cpp                      = /usr/bin/cpp
> include                  =
> define                   =
> integrator               = md
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 500000
> init_step                = 0
> comm-mode                = Linear
> nstcomm                  = 1
> comm-grps                =
> 
> bd-fric                  = 0
> ld-seed                  = 1993
> 
> emtol                    = 10
> emstep                   = 0.01
> nstcgsteep               = 1000
> nbfgscorr                = 10
> 
> nstxout                  = 1000
> nstvout                  = 1000
> nstfout                  = 1000
> nstcheckpoint            = 10000
> nstlog                   = 1000
> nstenergy                = 100
> nstxtcout                = 2000
> xtc-precision            = 10000
> xtc-grps                 =
> energygrps               =
> 
> nstlist                  = 1
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.2
> domain-decomposition     = no
> 
> coulombtype              = PME
> rcoulomb-switch          = 0
> rcoulomb                 = 1.2
> epsilon_r                = 1
> epsilon_rf               = 1
> vdw-type                 = Cut-off
> rvdw-switch              = 0
> rvdw                     = 1.2
> DispCorr                 = EnerPres
> table-extension          = 1
> energygrp_table          =
> fourierspacing           = 0.1
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = no
> 
> gb_algorithm             = Still
> nstgbradii               = 1
> rgbradii                 = 2
> gb_saltconc              = 0
> 
> implicit_solvent         = No
> 
> Tcoupl                   = no
> tc-grps                  = System
> tau_t                    = 0.1
> ref_t                    = 309
> Pcoupl                   = no
> Pcoupltype               = semiisotropic
> tau_p                    = 2.0
> compressibility          = 4.4395e-5  4.4395e-5
> ref_p                    = 1.01325  1.01325
> andersen_seed            = 815131
> 
> QMMM                     = no
> QMMM-grps                =
> QMmethod                 =
> QMMMscheme               = normal
> QMbasis                  =
> QMcharge                 =
> QMmult                   =
> SH                       =
> CASorbitals              =
> CASelectrons             =
> SAon                     =
> SAoff                    =
> SAsteps                  =
> MMChargeScaleFactor      = 1
> bOPT                     =
> bTS                      =
> 
> annealing                =
> annealing_npoints        =
> annealing_time           =
> annealing_temp           =
> 
> gen_vel                  = yes
> gen_temp                 = 309
> gen_seed                 = 1993
> 
> constraints              = hbonds
> constraint-algorithm     = Lincs
> unconstrained-start      = no
> Shake-SOR                = no
> shake-tol                = 1e-04
> lincs-order              = 5
> lincs-iter               = 2
> lincs-warnangle          = 30
> morse                    = no
> 
> energygrp_excl           =
> 
> disre                    = No
> disre-weighting          = Conservative
> disre-mixed              = no
> disre-fc                 = 1000
> disre-tau                = 0
> nstdisreout              = 100
> orire                    = no
> orire-fc                 = 0
> orire-tau                = 0
> orire-fitgrp             =
> nstorireout              = 100
> dihre                    = No
> dihre-fc                 = 1000
> dihre-tau                = 0
> nstdihreout              = 100
> 
> free-energy              = no
> init-lambda              = 0
> delta-lambda             = 0
> sc-alpha                 = 0
> sc-power                 = 1
> sc-sigma                 = 0.3
> 
> acc-grps                 =
> accelerate               =
> freezegrps               =
> freezedim                =
> cos-acceleration         = 0
> deform                   =
> 
> E-x                      =
> E-xt                     =
> E-y                      =
> E-yt                     =
> E-z                      =
> E-zt                     =
> 
> user1-grps               =
> user2-grps               =
> userint1                 = 0
> userint2                 = 0
> userint3                 = 0
> userint4                 = 0
> userreal1                = 0
> userreal2                = 0
> userreal3                = 0
> userreal4                = 0
> 
> 
> 
> 	
> 
> 	
> 		
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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