Quoting [EMAIL PROTECTED]: > Hi, > > I minimized without restraints, could that be the problem? > After the minimization I got a Potential Energy = -6.1434351e+02.
That seems fine. Basically, your lipid's headgroup is shearing itself apart (which you can tell from the LINCS warnings). At this point, I could only guess as to what's going wrong, which probably won't do you much good. If you'd like to send me your structure, topologies, and .mdp file off-list, I'd be happy to have a look at them. -Justin > > Gadi > > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > > 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 [email protected] > >> >> > 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 [email protected] > >> >> 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 [email protected] > >> > 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 [email protected] > >> 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 [email protected] > > 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 [email protected] > 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 [email protected] 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
