On Thu, Mar 21, 2013 at 8:56 AM, Shima Arasteh <shima_arasteh2...@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 -- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
