On 5/7/19 1:41 AM, ISHRAT JAHAN wrote:
---------- Forwarded message --------- From: ISHRAT JAHAN <jishra...@gmail.com> Date: Tue, May 7, 2019 at 11:05 AM Subject: atoms are not part of any of the T-Coupling groups To: <gromacs.org_gmx-users@maillist.sys.kth.se> Dear all, I am trying to calculate the lennard Jones interaction energy between protein and urea in the first solvation shell. I have made the index group of urea molecule in the first solvation shell and then tried to generate the .tpr file using that index. After running the command gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o prot_u3M_rerun -n water_urea_5ofprot.ndx following error occur- 35099 atoms are not part of any of the T-Coupling groups part of .mdp file and index file is given below rvdw = 1.2^M fourierspacing = 0.12^M fourier_nx = 0^M fourier_ny = 0^M fourier_nz = 0^M pme_order = 4^M ewald_rtol = 1e-5^M optimize_fft = yes^M ; Berendsen temperature coupling is on in two groups^M Tcoupl = V-rescale^M tc-grps = Protein Urea_5ofprot^M tau_t = 0.1 0.1 ^M ref_t = 300 300 ^M ; Energy monitoring^M energygrps = Protein Urea_5ofprot ; Isotropic pressure coupling is now on^M Pcoupl = berendsen^M and at the end of the Index file i have only added the residue index of urea within 5 of protein and save the index file.
While you can define whatever energygrps you like (note that the molecules will change over time and your results may end up being not useful), you need to couple all atoms in the system to a thermostat via tc-grps. Your urea selection is only a subset of the urea molecules, and if you have any other solvent, ions, etc. they are not being accounted for. tc-grps = Protein Non-Protein is almost always the way to go.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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-requ...@gromacs.org.
