[gmx-users] equilibrating a solvent

[Erik Lindahl]

Sidney Elmer wrote:

>I would appreciate any help anyone could give me on equilibrating a
>carbon tetrachloride solvent I made.  I've created the topology file and
>the .gro file, now I want to equilibrate it in an NVT ensemble.  What
>I've done is written a script that will create a
>crystal of the solvent.  I have checked to make sure that I've placed
>the necessary number of molecules in the box of a given volume to give
>the desired experimental density.  Now I just have to equilibrate the
>liquid.  In the .mdp file, whether I specify to use md with Berendson
>temperature coupling or stochastic dynamics, I get the same error
>message from grompp, which
>I have attached to this email.  There are 2560 atoms in the system, but
>for some reason, it appears that not all of the atoms are coupled to the
>
>heat bath.  As a side note, I noticed the first time I ran grompp, the
>error message specified that it was "Making dummy/rest group for
>T-Coupling containing 2555 elements" instead of the 2560.  That is why
>I'm thinking that some of the atoms aren't being coupled to the
>temperature bath, (but it may be unrelated).  I just don't understand
>the Fatal error:  Not enough ref_t and tau_t values.  I will also
>include the .mdp file for you as well.  I won't bother sending the .gro
>file, because it's pretty big, and it's sufficient to know that there
>are 2560 atoms in the file, and the box size is correct on the last
>line.  If you could help me I'd appreciate it.  Thanks.
>
>Sid
>
Hi Sid,

The first thing to do is probably an energy minimization. Use 
integrator=steep
and run say 100 steps, just to get rid on any atom overlaps. Turn off 
the constraints
during the energy minimization.

Once you have a reasonable (i.e., negative) energy, you can run SD or MD 
with
temperature coupling. The temperature coupling stuff seems to be 
commented out in your mdp file.
Try using e.g:

tcoupl = Berendsen
tc-grps = system
tau_t = 0.1
ref_t = 300

And turn of the pressure coupling to start with (keeping it commented 
out will do that). Once
you have equilibrated the box for a little while you can turn on 
pressure coupling too...


Cheers,

Erik