[gmx-users] System heating up during MD run? (Implicit solvent)

[Per Larsson]

Hi

There has been a number of reports lately about ill-behaving simulations using implicit solvent. I'm currently trying to investigate the cause of this, as such simulations used to work very nice in our hands.

In the meantime I would advice to use implicit solvent with caution.

Thanks
/Per

Skickat från min iPhone

30 okt 2011 kl. 02:10 skrev Matt Larson <larsonmattr at gmail.com>:

> I've been having problems getting implicit solvent systems (which are
> probably fairly experiment still in gromacs) to work correctly.  I've
> been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
> simulation.  By the end of the simulation, the temperature has risen
> from 300 K to 496 K - and the protein unfolds.  It was supposed to
> maintain temp at 300 K.
> 
> I have an a non-zero total charge of -6.999999.  With explicit
> solvent, I would normally add the appropriate matching ions, but with
> implicit solvent what should you do?   Could the non-zero total charge
> result in heating?  Or is the thermostat not working well enough
> (should I change tau-t or ref-t?)
> 
> Here is my md.mdp file:
> 
> 
> constraints         =  all-bonds ; trying..
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  1000000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         =  cut-off
> fourierspacing      =  0.16
> vdwtype             =  cut-off
> rcoulomb            =  1.0
> rvdw                =  1.0      ; important for neighbor searching
> pbc                 =  no       ; no periodic boundary conditions
> epsilon_rf          =  0
> rgbradii            =  1.0      ; must equal rlist, rcoulomb, rvdw
> comm_mode           =  angular
> optimize_fft        = yes
> 
> implicit_solvent    = GBSA
> gb_algorithm        = OBC
> gb_epsilon_solvent  = 80
> sa_surface_tension  = 2.25936
> 
> nstcomm         = 10
> nstxout         = 1000
> nstxtcout       = 1000
> nstvout         = 0
> nstfout         = 0
> 
> tcoupl              = andersen
> tc-grps             = system
> tau-t               = 0.1
> ref-t               = 300
> 
> gen_vel             = yes
> gen_temp            = 300
> gen_seed            = -1
> 
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