[gmx-users] T-Coupling groups in NVT

[Justin Lemkul]

On Thu, Mar 21, 2013 at 8:56 AM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> Hi,
>
> I am simulating a system of POPC/Water/Ions/protein.
> Ions are 1 M NaCL and 3 CL atoms to neutralize the system.
>
> In NVT step, I have coupling groups as :
> tc-grps        = Protein POPC    SOL_CL
>
> comm_grps    = Protein_POPC SOL_CL
>
> when I run the grompp for NVT, I get the error that the 615 Na atoms are
> not part of any of the T-Coupling groups.
>
> Now, I 'd like to know if I need to couple Na with SOL_CL such as
> SOL_CL-Na ? Or I need to create a seperate group for Na?
>
>
Ions should never be coupled separately from the solvent. You coupled Cl-
with water, why wouldn't you do the same for Na+?

http://www.gromacs.org/Documentation/Terminology/Thermostats

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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