Dear David, I am quite sure of both. To describe the situation more clearly, I copy-pasted below the coordinates of one molecule at a few stages of the simulation. In each case, after converting to gro, I checked with gmxdump that these are exactly the coordinates in .tpr and .xtc files.
How does mdrun decide on which atoms should be kept together? Perhaps I am missing something obvious here? 1) Initial configuration (from .tpr) ==================================== 127DPPC NC3 1513 4.939 0.585 6.960 127DPPC PO4 1514 4.565 0.271 6.959 127DPPC GL1 1515 4.456 0.318 6.508 127DPPC GL2 1516 4.106 0.404 6.414 127DPPC C1A 1517 4.379 0.296 6.060 127DPPC C2A 1518 4.469 0.468 5.752 127DPPC C3A 1519 4.771 0.477 5.404 127DPPC C4A 1520 4.983 0.731 5.051 127DPPC C1B 1521 3.928 0.449 5.934 127DPPC C2B 1522 4.024 0.485 5.487 127DPPC C3B 1523 4.341 0.499 5.190 127DPPC C4B 1524 4.535 0.629 4.899 2) At timeframe N (from .xtc) ============================= 127DPPC NC3 1513 4.099 0.003 6.747 127DPPC PO4 1514 4.011 0.320 6.473 127DPPC GL1 1515 4.341 0.200 6.056 127DPPC GL2 1516 4.136 0.434 5.918 127DPPC C1A 1517 4.584 0.090 5.635 127DPPC C2A 1518 4.554 0.154 5.241 127DPPC C3A 1519 4.530 0.190 4.756 127DPPC C4A 1520 4.611 0.251 4.352 127DPPC C1B 1521 4.073 0.173 5.607 127DPPC C2B 1522 3.945 -0.074 5.247 127DPPC C3B 1523 3.865 -0.358 4.900 127DPPC C4B 1524 3.613 -0.389 4.521 3) At timeframe N+1 (see y-coordinate) ====================================== 127DPPC NC3 1513 3.936 6.210 7.009 127DPPC PO4 1514 4.060 6.450 6.650 127DPPC GL1 1515 4.123 6.550 6.164 127DPPC GL2 1516 4.312 6.845 6.172 127DPPC C1A 1517 4.130 6.532 5.584 127DPPC C2A 1518 4.305 6.438 5.189 127DPPC C3A 1519 4.598 0.194 4.846 127DPPC C4A 1520 4.956 0.019 4.513 127DPPC C1B 1521 4.045 0.707 5.823 127DPPC C2B 1522 3.893 0.673 5.363 127DPPC C3B 1523 3.833 0.417 5.130 127DPPC C4B 1524 3.793 -0.035 5.205 Regards, Perttu On Wed, 22 Nov 2006, David van der Spoel wrote: > Perttu Niemelä wrote: > > Dear gmx-users, > > > > Is it true that mdrun (3.3.1) should not write broken > > molecules under any circumstances? If the .xtc output > > contains broken molecules, should one be worried? > > > > The molecules in my .xtc file are whole for the most of the > > time, but at some frames one or two are broken such that parts > > of the molecule are on opposite sides of the periodic box. I > > checked this with gmxdump and a short code of my own. Also, > > I was not able to make the molecules whole again with any of > > the -pbc options in trjconv. The molecules in the initial > > configuration are whole and I cannot see any reason for this. > > > > Best Regards, > > > > Perttu Niemela > > Helsinki Univ. Tech. > > Finland > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Are you sure that this is a single molecule *and* that the molecule was > not broken in the input? > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
