hi!
try doing minimization without SHAKE on.
--- blakrose.gazeta.pl wrote:
> Hello Dear Amber Users!
>
> Thaks for anwsering my questions.
> At this moment I have to ask some more questions :-)
>
> I have done minimisation in two ways (explicit and
> implicit water).
> I know the difference but how do I know which model
> is better?
> Should I decide about this looking at my output
> files?
>
> Here are some examples of my work trying to minimise
> my structure:
>
> 1) Explicit water without restrains:
>
> Input:
>
> &cntrl
> imin=1,
> maxcyc=2500,
> ncyc=500,
> cut=10.0,
> ntb=1,
> ntr=0,
> ntc=2, ntf=2
> /
>
> end of output:
>
> NSTEP ENERGY RMS GMAX
> NAME
> NUMBER
> 2500 -9.5821E+04 1.7828E+01
> 1.8903E+02
> H26 4186
>
> BOND = 160.8325 ANGLE = 751.0722
> DIHED
> = 2416.1475
> VDWAALS = 16711.7024 EEL = -126656.4899
> HBOND
> = 0.0000
> 1-4 VDW = 887.6797 1-4 EEL = 9907.5830
> RESTRAINT
> = 0.0000
>
>
>
> ( about 1400 steps:
>
> NSTEP ENERGY RMS GMAX
> NAME
> NUMBER
> 1400 -9.5822E+04 1.7829E+01
> 1.8923E+02
> H26 4186
>
> BOND = 160.8431 ANGLE = 751.0710
> DIHED
> = 2416.1423
> VDWAALS = 16712.1417 EEL = -126656.9667
> HBOND
> = 0.0000
> 1-4 VDW = 887.6811 1-4 EEL = 9907.5844
> RESTRAINT
> = 0.0000
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
> ) - Failure is not a good sign I think :-)
>
> 2) Implicit water (here cut is a bit bigger - trying
> on my own.. )
>
> Input:
>
> &cntrl
> imin=1, maxcyc=1000, ncyc=300,
> scee=1.2, cut=17.0, ntb=0,
> igb=1,
> /
>
> Output:
>
> NSTEP ENERGY RMS GMAX
> NAME
> NUMBER
> 1000 -1.1216E+04 1.3855E+00
> 5.9929E+01
> CG 1229
>
> BOND = 175.6606 ANGLE = 696.7887
> DIHED
> = 2259.0592
> VDWAALS = -2128.5296 EEL = -18267.1712
> EGB
> = -4605.8447
> 1-4 VDW = 843.8061 1-4 EEL = 9810.5691
> RESTRAINT
> = 0.0000
>
>
> 3) Minimisation in explicit water without restrains:
>
> Input:
>
> &cntrl
> imin=1, maxcyc=20000, ncyc=5000,
> scee=1.2, cut=17.0, ntb=2, ntp=1,
> dielc=1.0,
> nsnb=20,
> ntpr=5,
> &end
>
>
> Output:
>
> NSTEP ENERGY RMS GMAX
> NAME
> NUMBER
> 2960 -4.7799E+07 8.0983E+10
> 2.1738E+13
> H 4153
>
> BOND = 16488.2521 ANGLE = 844.0407
> DIHED
> = 2395.0702
> VDWAALS = 41551.6173 EEL = -287740.9301
> HBOND
> = 0.0000
> 1-4 VDW = 873.5359 1-4 EEL = *************
> RESTRAINT
> = 0.0000
>
>
>
-------------------------------------------------------------------
>
> I know my cut off is too big. It should be about
> 8-10.
> My minimisation steps should be much shorter. I
> think a good value
> is about maxcyc=2500 and ncyc=500 (but this is just
> my opinion).
>
> Please tell me if I have some more bad values in my
> inputs.
> Why in the explicit water the EEL is so big?
>
>
>
>
>
>
>
>
> --
> Tylko w sierpniu Avanti także w wersji MINI - z
> łatwością zmieści się w torebce!
> http://www.avantimoda.pl
>
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Received on Wed Aug 10 2005 - 09:53:00 PDT
