AMBER Archive (2006)

Subject: Re: AMBER: too big EEL values in the minimisation output

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Wed Nov 01 2006 - 12:08:27 CST

Dear Rachelle

If it were me I would stop the minimization at 300 steps, convert back to
a pdb file (ptraj) and look at the structure, particularly at close
contacts involving your HH atom. Does your HH have a charge?
How about its vdw parameters? Often hydrogens can get sucked into a
"Coulomb singularity"; that is, the distance between it and some
oppositely charged atom starts going to zero. Sometimes this is due to
bad initial placement (too close to that oppositely charged atom atom to
begin with) and sometimes to inadequate vdw repulsion for the hydrogen
atom (nothing to stop Coulomb's law from pulling it in). Those are the 2
causes I know of for your type of symptoms.
hope this helps
Tom Darden

On Wed, 1 Nov 2006, Rachel wrote:

> Dear AMBER users,
>
> I have a problem with my minimisation output, as u can see from the output
> below, ,from 250 step, the EEL value started to oscillate bewteen about
> (-2)*(10^6) to (-8)*(10^7) and then too big to fit the space, and the job
> stopped with the error message as 'MPI process rank, caught a SIGSEGV'. As
> can be seen, the problematic atom is atom 12159 which named HH (i made it
> up), it is a hydrogen atom in a hydrogen molecule that i added in my system.
>
> Can anyone suggest me what shall I do to solve the problem?
>
> Thanks very much in advance!
>
> Rachel
>
> The following is the output:
> -----------------------------------------------------------------------------------------------------------------------
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.8130E+05 8.6589E+00 1.2311E+03 DH 12158
>
> BOND = 12319.3157 ANGLE = 4262.2942 DIHED =
> 6788.2453
> VDWAALS = 20966.0238 EEL = -264399.8765 HBOND =
> 0.0000
> 1-4 VDW = 3817.5022 1-4 EEL = 34943.0628 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -1.8625E+05 2.8188E+00 4.3913E+02 FE 12110
>
> BOND = 11794.4274 ANGLE = 3181.7918 DIHED =
> 6832.5737
> VDWAALS = 18284.3228 EEL = -264556.0346 HBOND =
> 0.0000
> 1-4 VDW = 3581.8939 1-4 EEL = 34629.6021 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -1.8731E+05 1.4581E+00 8.3876E+01 FE 12110
>
> BOND = 11728.4379 ANGLE = 2852.5435 DIHED =
> 6858.0073
> VDWAALS = 17976.7772 EEL = -264680.1459 HBOND =
> 0.0000
> 1-4 VDW = 3457.5692 1-4 EEL = 34495.5597 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 150 -1.8797E+05 1.2138E+00 9.3236E+01 FE 12110
>
> BOND = 11714.1093 ANGLE = 2680.6319 DIHED =
> 6875.7728
> VDWAALS = 17802.4798 EEL = -264805.0722 HBOND =
> 0.0000
> 1-4 VDW = 3365.2133 1-4 EEL = 34401.7260 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 -1.8844E+05 1.4438E+00 2.2334E+02 FE 12110
>
> BOND = 11713.6752 ANGLE = 2577.4489 DIHED =
> 6887.9989
> VDWAALS = 17693.9506 EEL = -264938.4370 HBOND =
> 0.0000
> 1-4 VDW = 3294.3797 1-4 EEL = 34332.7427 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 250 -1.4001E+07 2.2874E+10 5.3567E+12 CB 1710
>
> BOND = 11724.6116 ANGLE = 2552.7526 DIHED =
> 6892.6022
> VDWAALS = 17660.7588 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 300 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4454 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 350 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.4475 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 400 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 450 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4465 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.4796 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 550 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 600 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4483 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 650 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.5746 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 700 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 750 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4500 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 800 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.5853 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 850 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 900 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4488 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 950 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.6284 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1000 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1050 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4489 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1100 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.6596 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1150 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1200 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4602 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1250 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.8262 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1300 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1350 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4600 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1400 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.7398 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1450 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1500 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4562 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1550 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.7172 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1600 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1650 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4629 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1700 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.8409 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1750 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1800 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4659 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1850 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.9068 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1900 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
>
> BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1950 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
>
> BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> 6892.6022
> VDWAALS = 17660.7584 EEL = -2031379.4671 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2000 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
>
> BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> 6892.6022
> VDWAALS = 17660.7587 EEL = -8509648.9202 HBOND =
> 0.0000
> 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 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