**From:** Price, Gareth (*Gareth.Price_at_warwick.ac.uk*)

**Date:** Thu Apr 18 2013 - 19:15:31 CDT

**Next message:**Thomas Brian: "Re: floating point reproduceability"**Previous message:**Norman Geist: "AW: floating point reproduceability"**In reply to:**Norman Geist: "AW: Minimisation of protein in a water box"**Next in thread:**Norman Geist: "AW: Minimisation of protein in a water box"**Reply:**Norman Geist: "AW: Minimisation of protein in a water box"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello

Firstly thank you for responding. Secondly, sorry for the delay in getting back to you!

I increased the number of minimization steps to 1000 and doubled the periodic boundary conditions – dimensions that should definitely be okay for my protein. I am rapidly heating the sample up to 310K – purely because I am not entirely sure how to slowly do it!

I looked at the Energy output: It quickly (within 50 timesteps) decreases by an order of magnitude but stays around there (from ~9e+09 to 2.5e+08).

I'm getting the same sort of output, though:

REINITIALIZING VELOCITIES AT STEP 1000 TO 310 KELVIN.

TCL: Running for 2500 steps

ERROR: Constraint failure in RATTLE algorithm for atom 2275!

ERROR: Constraint failure in RATTLE algorithm for atom 6562!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 1433!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 4127!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 4707!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Exiting prematurely; see error messages above.

====================================================

I am still stuck. If anyone would be willing to spare me a few minutes of your time I would really appreciate it. I can provide the files if necessary.

Thanks,

Gareth

________________________________________

From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Norman Geist [norman.geist_at_uni-greifswald.de]

Sent: 16 April 2013 07:31

To: 'Rajan Vatassery'

Cc: Namd Mailing List

Subject: AW: namd-l: Minimisation of protein in a water box

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-----
*

*> 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
*

*> >
*

*> >
*

*> >
*

**Next message:**Thomas Brian: "Re: floating point reproduceability"**Previous message:**Norman Geist: "AW: floating point reproduceability"**In reply to:**Norman Geist: "AW: Minimisation of protein in a water box"**Next in thread:**Norman Geist: "AW: Minimisation of protein in a water box"**Reply:**Norman Geist: "AW: Minimisation of protein in a water box"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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