<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear David:</div><div><br></div><div>Thanks a lot for your reply. You are absolutely right! All the charges in the tpr file is zero now. </div><div><br></div><div>This does not make much sense to me though, as the group I selected with "tpbconv" does not include all the atoms. I also tried to use other groups such as POPC or Protein and none of them give me sensible results (the charges are not all set to zero). Is this supposed to be a bug?</div><div><br></div><div>Thanks,</div><div>Bin</div><div><br></div><div><br><blockquote type="cite"><br>On 2010-12-03 08.45, BIN ZHANG wrote:<br><blockquote type="cite">Hi, all:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I was trying to use "tpbconv" to modify the tpr file with the command:<br></blockquote><blockquote type="cite">tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It basically sets the charge of one group to zero. However, when I<br></blockquote><blockquote type="cite">perform mdrun -rerun, all the coulombic energies are zeros, i.e.,<br></blockquote><blockquote type="cite">Coulomb-(SR), Coul.-recip. This really does not make sense since I still<br></blockquote><blockquote type="cite">have atoms in other groups that are charged. I was using gromacs4.0.7.<br></blockquote><blockquote type="cite"><br></blockquote>Please check using gmxdump that there still are charged groups left in your tpr file.<br><br><blockquote type="cite">Has anyone seen this before? What exactly is the correct way to zeroize<br></blockquote><blockquote type="cite">the charge for a group of atoms?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite">Bin<br></blockquote><blockquote type="cite"><br></blockquote><br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone:<span class="Apple-tab-span" style="white-space:pre"> </span>+46184714205.<br>spoel@xray.bmc.uu.se <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br><br><br><br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Olga Ivchenko <<a href="mailto:olga.ivchenko@gmail.com">olga.ivchenko@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">December 3, 2010 12:31:50 AM PST<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [gmx-users] proton proton transfer</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Reply-To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br></span></div><br><br>Hi Erik,<br>I think also I can try proton-proton transfer with gromacs later when it will be implemented.<br><br>best,<br>Olga<br><br><div class="gmail_quote">2010/12/2 Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span><br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Olga Ivchenko skrev 2010-12-02 13.30:<div><div></div><div class="h5"><br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Dear gromacs users,<br> <br> I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs.<br> I read about umbrella sampling, but may be there is other techniques?<br> <br> Yours sincerely,<br> Olga<br> </blockquote></div></div> I am working on a protocol to include proton transfer in classical gromacs simulations. Unfortunately it will note be ready for at least a month, so if you're in a hurry you'll have to do it with e.g. QM/MM.<br> <br> Erik<br> <br> -- <br> -----------------------------------------------<br> Erik Marklund, PhD student<br> Dept. of Cell and Molecular Biology, Uppsala University.<br> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br> phone: +46 18 471 4537 fax: +46 18 511 755<br> <a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br><font color="#888888"> <br> -- <br></font><div><div></div><div class="h5"> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br> Please don't post (un)subscribe requests to the list. 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