[gmx-users] Regarding tc-grps

[Anurag Dobhal]

Thank you Justin and Peter for the valuable inputs.




*Anurag Dobhal*
*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:

> Hi,
>
> 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.
>
>
> HTH,
>
> Peter
>
>
> 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*
> >
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

-- 


*DISCLAIMER:*

*This communication is intended only for the person or entity to which it 
is addressed and may contain confidential and / or privileged material. Any 
review, retransmission, dissemination or other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Any comments or statements made herein do not 
necessarily reflect those of Nanomedicine Research Group.  Before opening 
the email or accessing any attachments, please check and scan for virus.*