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

Reply via email to