Quoting [EMAIL PROTECTED]: > Hi, > > The full mdrun output when the simulation blows up is: > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max inf (between atoms 6 and 7) rms inf > bonds that rotated more than 30 degrees: > . > . > . > Warning: 1-4 interaction between 1 and 6 at distance > 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file
Basic information about this type of error can be found here (as well as several hundred posts in the list archive): http://wiki.gromacs.org/index.php/Errors#LINCS_warnings How did you do your minimization, with or without restraints? Did it converge to an acceptable potential energy? -Justin > > Thanks Gadi > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > > > > Did your minimization converge to a nice, negative potential energy? > > Also, what > > is the full mdrun output when the simulation blows up? You've > > quoted the last > > bit, but it would be more informative to see the whole output, or at least > a > > description of it (i.e., LINCS warnings). > > > > -Justin > > > > Quoting [EMAIL PROTECTED]: > > > >> > >> Hi, > >> > >> I tried using no temperature coupling and no constraints, that did not > help. > >> If I run the simulation without the position restraints it works OK. > >> Could there by something wrong with the posre file (I'll attach it at > >> the end of the email). > >> I want one of the atoms in the lipid to stay in one place and the rest > >> to wiggle around it. Is there any other way to do that which is not > >> position restraints. > >> > >> Thanks Gadi > >> > >> > >> [ position_restraints ] > >> ; atom type fx fy fz > >> 1 1 0 0 0 > >> 2 1 0 0 0 > >> 3 1 0 0 0 > >> 4 1 0 0 0 > >> 5 1 0 0 0 > >> 6 1 0 0 0 > >> 7 1 0 0 0 > >> 8 1 1000.0 1000.0 1000.0 > >> 9 1 0 0 0 > >> 10 1 0 0 0 > >> 11 1 0 0 0 > >> 12 1 0 0 0 > >> 13 1 0 0 0 > >> 14 1 0 0 0 > >> 15 1 0 0 0 > >> 16 1 0 0 0 > >> 17 1 0 0 0 > >> 18 1 0 0 0 > >> 19 1 0 0 0 > >> 20 1 0 0 0 > >> 21 1 0 0 0 > >> 22 1 0 0 0 > >> 23 1 0 0 0 > >> 24 1 0 0 0 > >> 25 1 0 0 0 > >> 26 1 0 0 0 > >> 27 1 0 0 0 > >> 28 1 0 0 0 > >> 29 1 0 0 0 > >> 30 1 0 0 0 > >> 31 1 0 0 0 > >> 32 1 0 0 0 > >> 33 1 0 0 0 > >> 34 1 0 0 0 > >> 35 1 0 0 0 > >> 36 1 0 0 0 > >> 37 1 0 0 0 > >> 38 1 0 0 0 > >> 39 1 0 0 0 > >> 40 1 0 0 0 > >> 41 1 0 0 0 > >> 42 1 0 0 0 > >> 43 1 0 0 0 > >> 44 1 0 0 0 > >> 45 1 0 0 0 > >> 46 1 0 0 0 > >> 47 1 0 0 0 > >> 48 1 0 0 0 > >> 49 1 0 0 0 > >> 50 1 0 0 0 > >> > >> Quoting Mark Abraham <[EMAIL PROTECTED]>: > >> > >> > [EMAIL PROTECTED] wrote: > >> > > >> > Please generate replies to the mailing list sensibly. It's very hard to > >> > work out who you are quoting where in this email. It'd be easy just to > >> > ignore it, and that's the last thing you should want. > >> > > >> >> Hello, > >> >> > >> >> I'm trying to run a simulation with one lipid molecule in a fixed > >> >> simulation box without pbc. > >> >> I set position restraints on one of the atoms and I seem to keep on > >> >> getting the following error: > >> > > >> > Why do you want MD of a single lipid and a position restraint on one > >> > atom? If you just want to see a lipid wiggle around, then don't create > >> > more numerical complexity. > >> > > >> >> The lipid is DPPC.The .itp file I got from a coworker that used it > >> >> before for membrane MD simulations. > >> >> To minimize the system I used steepest descent with the following > >> >> parameters: > >> > > >> > Well if your grompp and mdrun completed successfully and without > >> > warnings then you've probably got an OK topology and structure. > >> > > >> > The combination of all bond constraints, a single lipid in vacuo, > >> > temperature coupling and a single position restraint sounds like a > >> > recipe for a numerical disaster, i.e. blowing up. Try with fewer of > >> > those things applied, or get a more physically-reasonable system, like > >> > a whole membrane. > >> > > >> > Mark > >> > _______________________________________________ > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://www.gromacs.org/mailman/listinfo/gmx-users > >> > Please search the archive at http://www.gromacs.org/search before > posting! > >> > 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 > >> > >> > >> > >> ---------------------------------------------------------------- > >> This message was sent using IMP, the Internet Messaging Program. > >> > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> 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 > >> > > > > > > > > ======================================== > > > > Justin A. Lemkul > > Graduate Research Assistant > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > [EMAIL PROTECTED] | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > 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 > > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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