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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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