**From:** Norman Geist (*norman.geist_at_uni-greifswald.de*)

**Date:** Tue Apr 16 2013 - 01:31:31 CDT

**Next message:**Salvatore Mario Cosseddu: "Are coordinates in the tclForces module loaded as wrapped?"**Previous message:**Eric Lang: "RE: Problem with running FEP calculations"**In reply to:**Rajan Vatassery: "Re: Minimisation of protein in a water box"**Next in thread:**Price, Gareth: "RE: Minimisation of protein in a water box"**Reply:**Price, Gareth: "RE: Minimisation of protein in a water box"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

It's the Namd Plot Plugin, that can be used to plot the energies from the out, not to be confuses with Namd Energy. I agree with the other statements of Rajan.

~Norman Geist

*> -----Ursprüngliche Nachricht-----
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*> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
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*> Auftrag von Rajan Vatassery
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*> Gesendet: Montag, 15. April 2013 19:31
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*> An: Gareth Price
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*> Cc: namd-l_at_ks.uiuc.edu
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*> Betreff: Re: namd-l: Minimisation of protein in a water box
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*>
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*> Gareth,
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*> 100 steps is a small number of minimization steps for a very
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*> large
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*> system. Take a look at the energy of each step (graph it, you can
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*> possibly use NAMD Energy in VMD). If your system is still rapidly
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*> descending the PE surface, you'll need to probably add a few hundred
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*> more steps.
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*> Also, are you rapidly heating your sample (i.e. 0K -> 310K in 1
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*> step)?
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*> I don't think this will contribute to the problem you're reporting, but
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*> it may cause other problems down the road.
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*>
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*>
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*> Good luck,
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*>
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*>
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*> Rajan
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*>
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*>
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*>
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*>
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*> On Sat, 2013-04-13 at 19:52 +0100, Gareth Price wrote:
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*> > Hello
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*> >
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*> >
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*> > I am following the NAMD tutorial
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*> > (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-
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*> html/node9.html) to minimise my protein in a water box. When I run the
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*> actual NAMD program, with the attached conf.namd file, it quite quickly
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*> exits with the attached log file. Most importantly it terminates with:
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*> >
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*> >
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*> > LDB: ============= START OF LOAD BALANCING ============== 340.786
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*> > LDB: Largest compute 179 load 8.530063 is 10.0% of average load
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*> > 85.194022
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*> > LDB: Average compute 2.082990 is 2.4% of average load 85.194022
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*> > LDB: TIME 340.792 LOAD: AVG 85.194 MAX 131.415 PROXIES: TOTAL 24
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*> > MAXPE 7 MAXPATCH 3 None MEM: 3310.88 MB
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*> > LDB: TIME 340.797 LOAD: AVG 85.194 MAX 92.1218 PROXIES: TOTAL 24
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*> > MAXPE 7 MAXPATCH 3 TorusLB MEM: 3310.88 MB
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*> > LDB: ============== END OF LOAD BALANCING =============== 340.799
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*> > Info: useSync: 1 useProxySync: 0
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*> > LDB: =============== DONE WITH MIGRATION ================ 340.992
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*> > LINE MINIMIZER BRACKET: DX 1.62127e-09 1.002e-09 DU -5288.41 240.855
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*> > DUDX -1.1042e+14 -1.09678e+14 -1.09218e+14
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*> > PRESSURE: 100 1.33313e+09 -1.009e+07 3.3175e+07 -1.009e+07
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*> 1.29659e+09
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*> > -775795 3.3175e+07 -775795 1.34968e+09
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*> > GPRESSURE: 100 1.42554e+09 -9.55804e+06 3.11602e+07 -6.61256e+06
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*> > 1.38876e+09 -4.2318e+06 3.10716e+07 586571 1.44297e+09
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*> > Info: Initial time: 4 CPUs 3.23398 s/step 18.7151 days/ns 2533.11 MB
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*> > memory
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*> > ETITLE: TS BOND ANGLE DIHED
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*> > IMPRP ELECT VDW BOUNDARY
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*> > MISC KINETIC TOTAL TEMP POTENTIAL
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*> > TOTAL3 TEMPAVG PRESSURE GPRESSURE
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*> > VOLUME PRESSAVG GPRESSAVG
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*> >
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*> >
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*> > ENERGY: 100 933457.0735 200198.1313 8171.3299
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*> > 38969.5390 -67311.8822 351142159.9599 0.0000
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*> > 0.0000 0.0000 352255644.1514 0.0000
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*> > 352255644.1514 352255644.1514 0.0000 1326464790.2855
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*> > 1419090028.9051 74088.0000 1326464790.2855 1419090028.9051
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*> >
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*> >
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*> > REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
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*> > TCL: Running for 2500 steps
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 469!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 1!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 795!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 202!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 620!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 22!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 792!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Constraint failure in RATTLE algorithm for atom 36!
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*> > ERROR: Constraint failure; simulation has become unstable.
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*> > ERROR: Exiting prematurely; see error messages above.
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*> > ====================================================
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*> >
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*> >
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*> >
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*> >
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*> > I'm at an absolute loss as to why this is happening. I
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*> > Could someone help me with this, please?
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*> >
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*> >
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*> > I note that the initial values that are outputted in the log are very
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*> > high - is this the reason?
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*> >
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*> >
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*> > I have also found that this is talked about a bit in the
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*> > WIKI,
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*> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting
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*> , but nothing I do (in terms of adding margin, bigger PME box etc) is
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*> helping!
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*> >
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*> >
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*> > Thanks for your time,
*

*> > Gareth
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*> >
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*> >
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*> >
*

**Next message:**Salvatore Mario Cosseddu: "Are coordinates in the tclForces module loaded as wrapped?"**Previous message:**Eric Lang: "RE: Problem with running FEP calculations"**In reply to:**Rajan Vatassery: "Re: Minimisation of protein in a water box"**Next in thread:**Price, Gareth: "RE: Minimisation of protein in a water box"**Reply:**Price, Gareth: "RE: Minimisation of protein in a water box"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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