AMBER Archive (2006)

Subject: Re: AMBER: Energy differecnes as using igb=1 and igb=0

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Aug 10 2006 - 05:09:23 CDT

these energies are after 100 steps of MD (NSTEP) so they will certainly
differ when different solvent models are used. Compare the energies
at step 0 (use ntpr=1).

backy wrote:

> Hello:
> The both setting value of ntb are 0, so all the two system are not
> periodic.
> And the energy value difference is reflected in that way.
> igb=0:
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
>>> 100 -1.3078E+03 1.2304E+00 2.4978E+01 CZ 887
>>>
>>> BOND = 24.7837 ANGLE = 103.8203 DIHED = 573.6811
>>> VDWAALS = -499.1637 EEL = -4542.7328 HBOND = 0.0000
>>> 1-4 VDW = 246.7077 1-4 EEL = 2755.1466 RESTRAINT = 29.9078
>>> EAMBER = -1337.7571
>>
>
> igb=1:
>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 100 -2.1822E+03 1.4027E+00 5.2406E+01 CD 946
>>>
>>> BOND = 27.6833 ANGLE = 110.3090 DIHED = 570.5037
>>> VDWAALS = -474.1414 EEL = -4510.9973 EGB =
>>> -1095.9167
>>> 1-4 VDW = 249.6525 1-4 EEL = 2759.7612 RESTRAINT = 180.9595
>>> EAMBER = -2363.1456
>>
>
>
> Here is the input file igb=0;:
>
> minimize structure
> &cntrl
> imin=1, maxcyc=100,ncyc=1000,
> cut=999.0, igb=0
> ntpr=10, ntx=1, ntb=0,
> ntr=1,
> &end
> GROUP TITLE
> 10.0
> FIND
> * * M *
> * * S *
> * * B *
> * * 3 *
> * O * *
> * O2 * *
> * CB * *
> SEARCH
> RES 1 999
> END
> END
> =========================================================================
> Here is the input file igb=1:
>
> minimize structure
> &cntrl
> imin=1, maxcyc=100,ncyc=1000,
> cut=999.0, igb=1
> ntpr=10, ntx=1, ntb=0,
> ntr=1,
> &end
> GROUP TITLE
> 10.0
> FIND
> * * M *
> * * S *
> * * B *
> * * 3 *
> * O * *
> * O2 * *
> * CB * *
> SEARCH
> RES 1 999
> END
> END
> ====================================================================
>
> ----- Original Message ----- From: "Carlos Simmerling"
> <carlos_at_csb.sunysb.edu>
> To: <amber_at_scripps.edu>
> Sent: Wednesday, August 09, 2006 11:01 PM
> Subject: Re: AMBER: Energy differecnes as using igb=1 and igb=0
>
>
>> igb=0 might be doing a periodic boundary calculation on your
>> sytem. can you be more specific about exactly what you did?
>> what PME options did you use? Is your system periodic?
>> how large are the differences that you see?
>>
>> backy wrote:
>>
>>> Dear Amber users:
>>>
>>> If running two energy minimized calculations(AMBER 9), and the only
>>> difference is based on igb=1 and igb=0 respectively.
>>> My question is, why these two energy results were different not only
>>> in the EGB term but also slightly reflected in other energy terms.
>>> Thanks for helping.
>>>
>>>
>>>
>>> Sincerely.
>>>
>>> backy
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> igb=1;
>>>
>>>
>>>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 100 -2.1822E+03 1.4027E+00 5.2406E+01 CD 946
>>>
>>> BOND = 27.6833 ANGLE = 110.3090 DIHED = 570.5037
>>> VDWAALS = -474.1414 EEL = -4510.9973 EGB =
>>> -1095.9167
>>> 1-4 VDW = 249.6525 1-4 EEL = 2759.7612 RESTRAINT = 180.9595
>>> EAMBER = -2363.1456
>>> ===================================================================================
>>>
>>>
>>> igb=0;
>>>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 100 -1.3078E+03 1.2304E+00 2.4978E+01 CZ 887
>>>
>>> BOND = 24.7837 ANGLE = 103.8203 DIHED = 573.6811
>>> VDWAALS = -499.1637 EEL = -4542.7328 HBOND = 0.0000
>>> 1-4 VDW = 246.7077 1-4 EEL = 2755.1466 RESTRAINT = 29.9078
>>> EAMBER = -1337.7571
>>>
>>>
>>>
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>>
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