<div>Dear Zuzana,</div>
<div> </div>
<div>Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from both groups.</div>
<div> </div>
<div>Srinivs.<br><br><br></div>
<div class="gmail_quote">On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova <span dir="ltr"><<a href="mailto:Zuzana.Benkova@savba.sk">Zuzana.Benkova@savba.sk</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 16px">Dear GROMACS users,<br>I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. <br><br>
I want to compile a PEO chain centered in box of 2900 water molecules. <br><br>In my md.mdp the relevant section is as follows<br>Tcoupl = nose-hoover<br>tc-grps = PEO SOL<br>tau_t = 0.1 0.1<br>
ref_t = 50 50<br>gen_vel = yes<br>gen_temp = 50 50<br><br>I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using<br>
<br>grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50K<br><br>and got message<br><br>Program grompp, VERSION 4.0.3<br>Source code file: readir.c, line: 1050<br><br>Fatal error:<br>
16 atoms are not part of any of the T-Coupling groups<br><br>I tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same. <br><br><br> I would be really thankful for an advice which can move me further. Thank you in advance.<br>
<br>Zuzana<br><br><br><br></div><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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J. Srinivasa Rao Ph.D.<br>Post-doctoral Research Associate<br>C/o Prof. Luis R Cruz Cruz<br>Computational Biophysics Group<br>Department of Physics<br>Drexel University<br>3141 Chestnut St<br>Philadelphia, PA 19104, USA.<br>
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