<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Aug 16, 2010, at 1:33 PM, Anirban Ghosh wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option with mdrun, right? </blockquote>yes<br><blockquote type="cite">And why does this curvature of the membrane occurs?</blockquote>No idea!<br><blockquote type="cite"><div><br></div><div>Thanks a lot once again.</div><div><br></div><div> Regards,</div><div><br></div><div>Anirban<br><br><div class="gmail_quote">On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"> <br> Although a bit worrying the curvature of your bilayer is not<br> responsible for the error message you are seeing.<br> <br> to solve the problem you have to increase to use the -rrd option<br> (see manual for explanation). Typicaly a value of 1.4 to 1.6 should<br> be fine.<div><div></div><div class="h5"><br> <br> On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote:<br> <br> </div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5"> Hi ALL,<br> <br> I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error:<br> <br> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> Energies (kJ/mol)<br> Bond G96Angle Proper Dih. Improper Dih. LJ (SR)<br> 4.73694e+04 3.00928e+04 4.68451e+03 8.26028e+02 -1.29727e+06<br> Coulomb (SR) Potential Kinetic En. Total Energy Temperature<br> -7.97216e+03 -1.22227e+06 2.24656e+05 -9.97613e+05 3.21675e+02<br> Pressure (bar) Cons. rmsd ()<br> -9.97540e+00 1.69233e-05<br> <br> <br> Not all bonded interactions have been properly assigned to the domain decomposition cells<br> <br> A list of missing interactions:<br> G96Angle of 28064 missing 1<br> <br> Molecule type 'DSPC'<br> the first 10 missing interactions, except for exclusions:<br> G96Angle atoms 10 11 12 global 5309 5310 5311<br> <br> -------------------------------------------------------<br> Program mdrun_mpi, VERSION 4.0.7<br> Source code file: domdec_top.c, line: 341<br> <br> Fatal error:<br> 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck<br> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> <br> On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as:<br> <br> --------------------------------------------------------------------------------------------------------------<br> [ system ]<br> PROT in DSPC Bilayer<br> <br> [ molecules ]<br> Protein 1<br> DSPC 104<br> W 1397<br> NA+ 0<br> CL- 4<br> Protein 1<br> DSPC 104<br> W 1397<br> NA+ 0<br> CL- 4<br> -------------------------------------------------------------------------------------------------------------<br> <br> How can I resolve this error? Any suggestion is welcome.<br> <br> Regards,<br> <br> Anirban<br></div></div> <sim.jpeg>--<br> 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/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote> <br> -- <br> 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/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use thewww interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote></div><br></div> -- <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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<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</blockquote></div><br></body></html>