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On 11/23/11 5:43 PM, sarah k wrote:
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cite="mid:CAA1O8UBCQCePN9YLJKw2edmyWiW9Veo8WZuoo3oZ9_x8610dUA@mail.gmail.com"
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<div>Dear Gromacs Users,</div>
<div> </div>
<div>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:</div>
<div> </div>
<div>mdrun -s A_pr.tpr -o A_pr.trr -c A_b4md.gro -g pr.log -e
pr.edr&</div>
<div>==> the error: too many LINCS warnings </div>
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Could be a sign something is going wrong with your system. Did you
do a proper energy minimization?<br>
Check the gromacs error pages for some more precise indication.<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
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cite="mid:CAA1O8UBCQCePN9YLJKw2edmyWiW9Veo8WZuoo3oZ9_x8610dUA@mail.gmail.com"
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<div> </div>
<div>For protein B I have to add 4 NA+:</div>
<div>grompp -f pr.mdp -c B_b4pr.gro -p B.top -o B_pr.tpr</div>
<div>==> error: 4 atoms are not part of the T-coupling groups.</div>
<div> </div>
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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<br>
<br>
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cite="mid:CAA1O8UBCQCePN9YLJKw2edmyWiW9Veo8WZuoo3oZ9_x8610dUA@mail.gmail.com"
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<div>I checked my pr.mdp file. Tcoup is berendsen. </div>
<div> </div>
<div>How can I solve these problems?</div>
<div> </div>
<div>Best regards,</div>
<div>Sarah</div>
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<pre class="moz-signature" cols="72">--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
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