[gmx-users] Annealing doesn't work with Andersen thermostat?

[Michael Shirts]

Hi, William-

Interesting.  There's too many conditionals with the current patchwork
of temperature control methods, so there is an ongoing (though too
slow) effort to reorganize the algorithms to eliminate such errors as
this.

For a medium-term solution, I'd suggest filing a redmine issue
(redmine.gromacs.org) on this error so that it gets fixed for the next
round of update.

In the short-term, if you are interested in introducing stochasticness
into the annealing, I'd suggest using the sd integrator for now.

On Mon, Feb 3, 2014 at 3:02 PM, William Welch <wwelch000 at gmail.com> wrote:
> Hi,
> I am doing some simulations on simple Lennard-Jones spheres and course
> grained hydrocarbon models. I have been using the annealing utility
> successfully until I switched from the V-rescale thermostat to the Andersen
> thermostat. When I use the Andersen thermostat, the system gets to the
> first temperature and then stays there. This does not happen if I switch to
> a different thermostat. My guess is that Andersen not available with
> annealing, at least in the version I'm using (4.6) , however I have not
> been able to find any reference to that online or in the mailing list. Here
> is one of the mdp files that produced a simulation that did not work. .
>
>  title               =  8pore
> integrator          =  md-vv
> dt                  =  0.003    ; ps !
> nsteps              =  2500000  ; total 7500 ps.
> nstcomm             =  1
> nstxout             =  2000
> nstvout             =  2000
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  1
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.5
> rcoulomb            =  1.5
> rvdw                =  1.5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  Andersen
> tc-grps             =  LJ BL
> tau_t               =  0.1 0.1
> ref_t               =  230 230
> ; Energy monitoring
> energygrps           =  LJ BL
> energygrp-excl       =  BL BL
> freezegrps           =  BL
> freezedim            =  Y Y Y
> ; Isotropic pressure coupling is now on
> ;Pcoupl              = berendsen
> ;Pcoupltype          = isotropic
> ;tau_p               =  0.5
> ;compressibility     =  4.5e-5
> ;ref_p               =  1.0
> annealing            = single single
> annealing-npoints    = 20 20
> annealing-time       = 0 200 400 800 1200 1600 2000 2400 2800 3200 3600
> 4000 4400 4800 5200 5600 6000 6400 6800 7200  0 200 400 800 1200 1600 2000
> 2400 2800 3200 3600 4000 4400 4800 5200 5600 6000 6400 6800 7200
> annealing-temp       = 100 200 230 240 250 260 270 280 290 300 310 320 330
> 340 350 360 370 380 390 400 100 200 230 240 250 260 270 280 290 300 310 320
> 330 340 350 360 370 380 390 400
> ;Generate velocites is off at 300 K.
> gen_vel             =  yes
> gen_temp            =  230.0
> ;gen_seed           =  173529
>
> Velocities are generated at 230 (which is kind of strange, but changing
> that doesn't do anything) and the system cools to 100K and then stays
> there. The output in the md.log file shows that the correct ref_t is being
> read, but the actual temperature of the system does not increase. The same
> input using the md integrator and the V-rescaling thermostat does what it's
> supposed to.
> Will
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.