[gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

[ISHRAT JAHAN]

Thank you Justin sir for the reply. I have resolved my problem.

On Wed, May 8, 2019, 5:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/7/19 1:41 AM, ISHRAT JAHAN wrote:
> > ---------- Forwarded message ---------
> > From: ISHRAT JAHAN <jishrat17 at 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 at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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