[gmx-users] equilibrating a solvent

Sidney Elmer sidnasty at stanford.edu
Tue Jun 18 04:11:46 CEST 2002

Hi Erik,

I found the problem.  It was in my index file.  I didn't write a number for
each atom in the system, my bad.  Thanks.

Erik Lindahl wrote:

> 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

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