Chris, As you suggested, I ran it on one node, and it still blew up, so it appears to be some oddity with the constraint that I am imposing.
When I look at the dgdl.xvg file from the run, there appear to be a number of transient spikes that are a couple orders of magnitude larger than the typical variation during the run, and I am getting errors on an angle changing by more than 30 degrees as a LINCS warning during those short spikes. The final system blow-up starts with the same situtation, which degenerates into a full blow system explosion, with bond lengths going to crzy high values. So my question boils down to this: What is it about a type 2 constraint that will generate these ridiculously large forces on relatively rare occasions? Or perhaps, what error am I making in setting up the simulation that would cause only the constrained system to manifest this behavior? Warren Gallin On 2010-05-27, at 11:22 AM, chris.ne...@utoronto.ca wrote: > Dear Warren: > > I don't have your answer, but I'll point out that when you ask: "Is it > possible that this is a problem that arises because of domain decomposition > over multiple nodes" that you are probably the person in the best position to > address this. 300ps should not take too long to simulate so why not try it on > a single node and also on multiple nodes with mdrun -pd and report back? > > Somebody may have your answer, but the system blowing up question is so > common that it is probably faster for you to rule out some things first. > > Chris. > > -- original message -- > > I am looking at the the free energy profile of end-to end distances of > various peptides, but I am consistently getting a system blow-up when running > simulations with that distance constrained by a type 2 constraint. > > I run a simulation of the unconstrained peptide in a box of tip4p > water, Na+ and Cl- ions, and it runs with no problem. > > Then I grab a frame of that simulation in which the end-to-end distance > is 0.8 nm (full frame including water) as a .gro file. Then I add a type 2 > constraint between the N-terminal nitrogen atom and the C-terminal carboxyl > carbon, create a new .tpr file using the revised topology and the already > equilibrated frame as starting files and a .mdp file that now has the > free_energy set to on, and then launch mdrun. > > About 189 ps into the simulation I start getting warnings as follows, > ultimately leading to blow-up and the run failing (fragment of error file > output shown at end of message). > > I am obviously missing something about how the constraint is handled. > Is it possible that this is a problem that arises because of domain > decomposition over multiple nodes, ir is there something more basic that > needs to be dealt with when imposing a type 2 constraint? > > Warren Gallin > > Step 94636, time 189.272 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.041028, max 0.161215 (between atoms 217 and 219) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > > Step 94637, time 189.274 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.018884, max 0.100333 (between atoms 217 and 218) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > > <SNIP> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php