Re: Minimisation of protein in a water box

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Mon Apr 15 2013 - 12:30:46 CDT

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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