[gmx-users] Regarding tc-grps
anurag.dobhal at nano-medicine.co.in
Fri Sep 30 07:46:53 CEST 2016
Thank you Justin and Peter for the valuable inputs.
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
On Thu, Sep 29, 2016 at 8:25 PM, Peter Kroon <p.c.kroon at rug.nl> wrote:
> please see http://www.gromacs.org/Documentation/Terminology/Thermostats
> The number of molecule types (what you call groups?) in your .top file
> are not relevant for the number of tc groups you make.
> You need to make sure your system obeys a boltzmann distribution (or
> maxwell? I'm not sure). In principle a single temperature coupling group
> is always enough, but the exchange of thermal energy between i.e. a
> protein and the surrouding solvent may not be efficient enough to make
> sure that this is true. In such a case people use two (or more)
> temperature coupling groups.
> To sum up: your system as a whole needs to obey a certain distribution
> of kinetic energy. In addition, every "subsystem" (i.e. protein or
> solvent or any combination thereoff) needs to obey such a distribution
> as well.
> In your case, I think a single tc group (System) should be enough.
> On 29-09-16 16:31, Anurag Dobhal wrote:
> > Dear Gromacs users,
> > I am simulating a polymer chain without any solvent using OPLS AA force
> > field, how many tc-grps should I put in the .mdp file ? as there is only
> > one 1 group in the topol.top file.
> > Thank You
> > *Anurag Dobhal*
> > *Graduate Student (Bioprocess Technology)*
> > *Institute of Chemical Technology, Mumbai*
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