On 11/23/11 5:43 PM, sarah k wrote:
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
Could be a sign something is going wrong with your system. Did you do a
proper energy minimization?
Check the gromacs error pages for some more precise indication.
http://www.gromacs.org/Documentation/Errors
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.
Control the groups of your thermostat in your .mdp file. There should be
one including the whole system. Check section 7.3.14 of the gromacs manual
I checked my pr.mdp file. Tcoup is berendsen.
How can I solve these problems?
Best regards,
Sarah
--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
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