[gmx-users] Re: heating the system

[nk yx]

Hi,Anton
   Do you mean that it'd better use 'simulated annealing' method to heat 
the system with the zero_temp_time set to negtive? If i want to heat the 
system from 0K to 100K during 10ps period, how do i set up the parameters 
of heat.mdp?
  dt=0.002ps
  nsteps=5000
  annealing=yes
  zero_temp_time=?
  ref_t=?(0K or 100K)
 Is it so kind of you to tell me the last two parameters?
 Thank you very much!

Best wishes,
nkyx
  








>> >>Hi,all
> >>  I am a new user for Gromacs. After minimization, I want to heat my
> >>system from 0K ,100K,200K to 300K in a short period(e.g.30ps). However,
>[...]
> > there's nothing wrong with your mdp's, it's normal that ref_t is 
reached
> > within a few timesteps.
> > i'm just wondering why you do it that way.
> >
> > If you just want to get the md started after em use:
> > ref_t=300, gen_vel=yes, gen_temp=300
> > (maybe use pressure coupling to allow scaling of the box)
> >
> > If you really want to heat up slowly (for whatever reason)
> > use a larger value for tau_t.
>
>No - you should use the heating/cooling option provided with
>the 'simulated annealing'. Check the mdp options page in the
>online manual.
>
>Beware that Berendsen T couping can result in unequally
>partitioned kinetic energy. For starting normal simulations,
>I'd strongly recommend to generate velocities, the way
>Christoph describes.
>


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