AW: Minimisation of protein in a water box

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Apr 16 2013 - 01:31:31 CDT

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

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

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