[gmx-users] T-coupling

Gianluca Santoni gianluca.santoni at ibs.fr
Wed Nov 23 11:03:40 CET 2011

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.
> 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
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

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