[gmx-users] System heating up during MD run? (Implicit solvent)
per.larsson at sbc.su.se
Mon Oct 31 09:19:06 CET 2011
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.
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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