AMBER Archive (2006)Subject: Re: AMBER: Energy differecnes as using igb=1 and igb=0
From: backy (backy_at_ibms.sinica.edu.tw)
Date: Thu Aug 10 2006  01:47:37 CDT
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
>> 14 VDW = 246.7077 14 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
>> 14 VDW = 249.6525 14 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
>> 14 VDW = 249.6525 14 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
>> 14 VDW = 246.7077 14 EEL = 2755.1466 RESTRAINT = 29.9078
>> EAMBER = 1337.7571
>>
>>
>>
>> 
>> The AMBER Mail Reflector
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>
> 
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