Thank you Justin sir for the reply. I have resolved my problem. On Wed, May 8, 2019, 5:57 PM Justin Lemkul <jalem...@vt.edu> wrote:
> > > 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. > -- 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.