<br><br><b><i>David van der Spoel <spoel@xray.bmc.uu.se></i></b> skrev:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Soren Enemark wrote:<br>> Hi,<br>> maybe I am misunderstanding either the manual or the topic.. but - in <br>> my world -<br>> I never stop being puzzled by the part of chapt 6 in the manual which <br>> apparently<br>> says that such distance constraining is possible even though it (seems) <br>> to be<br>> secretly known that it is _not_ possible unless one uses the method <br>> suggested<br>> below.<br>> I believe, I suggest adding a comment in the manual.<br>> <br><br>can you be more specific which part of the manual you mean?<br><br> Basically almost anywhere in chapter 6 from 6.1 to 6.25 included.<br> <br> I mean, pulling works between 2 different molecules, why is it then obvious that constraining doesn't?<br> <br> <br> <br>>
-Soren<br>> <br>> */Tsjerk Wassenaar <tsjerkw @gmail.com="">/* skrev:<br>> <br>> Hi Kanin,<br>> <br>> The only way to get away with that is to merge your two parts to form<br>> one molecule, with the only connection being a distance_restraint (or<br>> another bonded term if you want to emulate bond-like behaviour such as<br>> a salt-bridge).<br>> <br>> Best,<br>> <br>> Tsjerk<br>> <br>> On 9/11/06, kanin wichapong wrote:<br>> > Dear All<br>> > I would like to know how to constraint the distance between the<br>> > different molecule, ex. the ligand and the protein. As far as I know<br>> > whatever to do the constraint, distance, angle dihedral, it can<br>> do just in<br>> > the same molecule.<br>> > Thank you in advance for all of your help.<br>> ><br>> > With Best all regard,<br>> >
Kanin<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read<br>> > http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> ><br>> <br>> <br>> -- <br>> <br>> Tsjerk A. Wassenaar, M.Sc.<br>> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>> Dept. of Biophysical Chemistry<br>> University of Groningen<br>> Nijenborgh 4<br>> 9747AG Groningen, The Netherlands<br>> +31 50 363 4336<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>>
http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> <br>> ------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><br>-- <br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala
University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br>spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></tsjerkw></blockquote><br>