AMBER Archive (2004)

Subject: RE: AMBER: Spike in energy and RMS

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Sep 08 2004 - 09:37:26 CDT

Dear Balvinder,

The behaviour you describe is not normal. There is most probably either
something wrong with the system you are simulating or something wrong with
your installation of amber. Have you tried running the test cases? Do they
all pass?

If all the tests pass then can you please post your prmtop and inpcrd files
so that I can try it out.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Balvinder Singh
> Sent: 08 September 2004 15:49
> To: amber_at_scripps.edu
> Subject: AMBER: Spike in energy and RMS
>
>
>
> I am minimizing a protein using AMBER 7 on IRIX platform. During
> minimization, the energy sharply rises at a single step and
> then returns
> to lower value on the very next step. Analysis shows bond and angle
> energy increases sharply as compared to other energies. And this is
> repeated at every 25th step. The output shows similar pattern
> of spike in
> energy and RMS with IGB=one as well. However, at the end, the
> minimization
> converges to a visually normal structure meeting convergence criteria.
>
> Is this behaviour normal? Can anyone explain it?
>
> -Balvinder
>
> The input is as follows:
>
> &cntrl
> imin=1, maxcyc=65000, ncyc=12000, dielc=4,
> drms=0.0005, ntb=0, cut=50, ntpr=1, ntwx=500, ntwr=500,
> &end
> &ewald
> eedmeth=5,
> &end
>
>
> A part of the output:
>
> .
> .
> .
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 21204 7.7982E+01 1.3034E-02 2.2445E-01 HH12 423
> BOND = 24.0978 ANGLE = 97.6317 DIHED = 514.6982
> VDWAALS = -544.7447 EEL = -370.6831 HBOND = 0.0000
> 1-4 VDW = 215.7988 1-4 EEL = 141.1831 RESTRAINT = 0.0000
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 21205 4.8300E+02 2.5692E+01 3.0659E+02 C 550
> BOND = 349.9796 ANGLE = 167.3124 DIHED = 518.1113
> VDWAALS = -542.3081 EEL = -369.2192 HBOND = 0.0000
> 1-4 VDW = 219.0747 1-4 EEL = 140.0487 RESTRAINT = 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 21206 7.7981E+01 2.8785E-02 3.2231E-01 C 550
> BOND = 24.1048 ANGLE = 97.6212 DIHED = 514.6983
> VDWAALS = -544.7441 EEL = -370.6810 HBOND = 0.0000
> 1-4 VDW = 215.8008 1-4 EEL = 141.1812 RESTRAINT = 0.0000
> .
> .
> .
> ------------------------------------
>
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu