RE: NAMD 2.6 - PME Error on Large Protein-DNA System!

From: Sean Law (
Date: Thu Feb 28 2008 - 11:35:42 CST

Hi Peter,
Thank you for the prompt reply.
I looked into it but I couldn't quite figure out how to respond directly to the NAMD list with repsect to my original post so I hope it makes its way there. Yes, I am using langevin dynamics so you are correct about the reproducability of the simulation. One thing that I failed to point out is that at the input to NAMD was derived from initial setup from CHARMM. That is, the system was setup (minimized, heated up, equilibrated for 5 ns) using CHARMM but after realizing the long-term efficiency and better parallelization in NAMD I decided to switch over. I am not sure if this would affect anything so please correct me if I'm wrong. Furthermore, I have switched from using NVT in CHARMM to NPT in NAMD. Starting from the equilibrated system (derived from CHARMM), I've used NAMD to simulate it and examined the boxsize/cell size (PME Grid 128 x 96 x 96) as per your suggestion. Being an NPT system, I expect the size to fluctuate a little (which it does) but not a lot. From the log file, the volume fluctuates but is relatively the same and the cell size at the end of each run (including several restarts) are as roughly follows: Starting Structure ---> 155 x 117 x 94 for 20 psRestart 1 -----------> 152 x 115 x 92 for 7 psRestart 2 -----------> 152 x 115 x 92 for 3.85 psRestart 3 -----------> 152 x 115 x 92 for 3.85 ps:::Restart 13 ----------> 152 x 115 x 92 for 3.85 psRestart 14 ----------> Stray PME grid charges detected at 2.22 ps Note: In this set of test runs, the "useFlexibleCell" option was turned on with a 0.001 ps timestep. I'm not sure if this answers your questions but from the results obtained from my previous tests, the boxsize/cell size appears to have equilibrated after the first 20 ps and the run does restart and is capable of going for a while (approximately 95 ps) before hitting the same error. Finally, is there any correlation between using the "+netpoll" option and having a successful run? Thank you for your time. SeanMichigan State University > Date: Wed, 27 Feb 2008 23:59:41 -0600> From:> To:> CC:;;> Subject: Re: namd-l: NAMD 2.6 - PME Error on Large Protein-DNA System!> > Hi Sean,> > >> > > > I did some digging and tried the following (while supplying the SAME > > random seed to keep things consistent):> Please note that if you're doing langevin dynamics in parallel, this > still doesn't guarantee identical results because of non-determinism in > communication ordering and the way the NAMD rng works. There have been a > few threads in the past 6 months on namd-l on this subject, if you're > interested.> > > > > > I would really appreciate if anybody could help explain this behaviour > > and welcome any comments, questions, or feedback that would help solve > > this problem! > > > Given the troubleshooting you've already tried (and thank you for noting > what you've done!), the next likely culprit is changes in your periodic > cell size that are too large. I'd recommend checking two things:> -see how much your periodic cell size changes over the course of the run> -if you restart your simulation from the restart files saved before the > crash, does it run fine or crash again?> > This should (hopefully) help to find whatever is going on here.> > Best,> Peter>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:47:36 CST