[gmx-users] T-coupling

sarah k dailycolors at gmail.com
Wed Nov 23 10:43:39 CET 2011

Dear Gromacs Users,

I need to simulate two protein structures by Gromacs 5.4.0. For protein A,
the net charge is zero so I don't add any ions. All the commands work
properly unitil mdrun of the A_pr.tpr:

mdrun -s A_pr.tpr -o A_pr.trr -c A_b4md.gro -g pr.log -e pr.edr&
==> the error: too many LINCS warnings

For protein B I have to add 4 NA+:
grompp -f pr.mdp -c B_b4pr.gro -p B.top -o B_pr.tpr
==> error: 4 atoms are not part of the T-coupling groups.

I checked my pr.mdp file. Tcoup is berendsen.

How can I solve these problems?

Best regards,
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