[gmx-users] V-rescale fatal error

[Justin Lemkul]

On 3/19/19 6:30 PM, Adriana Garro wrote:
> Dear all,
>
> I am performing MD simulations on a small system:
> peptide (9 residues) + TFE + Water + CL to finally evaluate the peptide
> secondary structure in this solvent mix. When a try to equilibrate the
> system, nvt, I get a fatal error
>
>> * The v-rescale thermostat was called with a group with #DOF=2.999250, but
> *>* for #DOF<3 only integer #DOF are supported
> *>
>
> I have found that it's a bug but I don't know how I should proceed to
> avoid this.
>
> My temperature coupling groups are (from nvt.mdp file):
>
> * Temperature coupling is on
> Tcoupl                      = V-rescale
> tc-grps                     = protein TFE sol CL
> tau_t                       = 0.1 0.1 0.1 0.1;
> ref_t                       = 300 300 300 300; *
>
> * I could not find much **information about it online.*

Do not couple everything separately. "Protein Non-Protein" should work 
fine in most cases.

See 
http://manual.gromacs.org/current/user-guide/terminology.html#thermostats 
under "What not to do"

-Justin

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Justin A. Lemkul, Ph.D.
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