[gmx-users] energy conservation

[Erik Marklund]

Hi,

Switch to double precision, and shorten the timestep or use constraints. 
Otherwise the conserved energy will drift for such a system.

Erik

Gavin Melaugh skrev 2011-06-06 10.56:
> Hi all
>
> I have run a very long NVT simulation>500ns of one molecule (220 atoms)
> to try to assess the fluctuations in a particular event. When I analyse
> the energies it seems that the conserved quantity drifts significantly.
> Why would this be? Has it got to do with the thermostat I am using?
> Please find below  the mdp file.
>
>
> title       = Pull test
> cpp         =
> include     =
> define      =
> integrator  = md
> nsteps      = 300000000
> dt          = 0.001
> nstxout     = 150000
> nstvout     = 150000
> nstlog      = 150000
> nstenergy   = 15000
> nstfout     = 150000
> pbc         = no
> nstlist     = 0
> ns_type     = simple
> vdwtype     = cut-off
> rlist       = 0
> rvdw_switch = 0
> rvdw        = 0
> coulombtype = cut-off
> rcoulomb    = 0
> tcoupl      = nose-hoover
> tc_grps     = system
> tau_t       = 0.1
> ref_t       = 400
> gen_vel     = no
> gen_temp    =
> constraints = none
> comm_mode   = angular
>
> Cheers
>
> Gavin


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/