[gmx-users] System heating up during MD run? (Implicit solvent)
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 31 11:41:56 CET 2011
I would also add that the settings provided below probably produce severe cutoff
artifacts. In my experience, the only stable settings are those of the
all-vs-all kernel (with infinite cutoffs).
-Justin
Per Larsson wrote:
> 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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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