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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Lab: 303 Engel Hall
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