AW: Minimisation of protein in a water box

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Apr 19 2013 - 02:03:15 CDT

Hi,

I think you are really new to md right?

I will just put my comments out and hope it will help.

The number of steps a minimization needs to find a minimum depends on system
size. The bigger the system, the longer the minimization should run. It's
not unusual to run it from 10000 to 100000 steps. To verify that a
minimization has been running for long enough, you can check the TOTAL
energy in the output (VMD NAMD-Plot). This value should get constant. It
will no more change before comma and not in the first 4-6 digits behind the
comma. When a minimization starts, the energy will fall rapidly and the
decrease in energy converges. This means, that the full energy plot is
scaled by the initial rapid decrease and "looks" linear afterwards. But this
is not the case. The energy is still falling, but less rapid. If you zoom
into the graph you can see that it's still decreasing by thousands in a few
steps. This means, you minimization time is still too short.

Additionally 9e+09 to 2.5e+08 is a HUGE range !!

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Price, Gareth
> Gesendet: Freitag, 19. April 2013 02:16
> An: Norman Geist; 'Rajan Vatassery'
> Cc: Namd Mailing List
> Betreff: RE: namd-l: Minimisation of protein in a water box
>
> 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
> > >
> > >
> > >
>
>
>

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