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

[Justin A. Lemkul]

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
>>
>> -----
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
========================================

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

========================================