[gmx-users] equilibrating a solvent

Erik Lindahl lindahl at stanford.edu
Tue Jun 18 01:05:26 CEST 2002

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.
Hi Sid,

The first thing to do is probably an energy minimization. Use 
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 
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...



More information about the gromacs.org_gmx-users mailing list