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Re: Termination in equilbrium when heating
rmv #37942 06/21/20 02:15 PM
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Thanks,my teacher. Thank you for your suggestions and your time. And this time I tried again and again.

I used SHAKE BONH PARAM at initial minimization before solvation, but I found the energy was higher than previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9 ). So which one is better?

Previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 3311-238148.54483 -0.00000 0.00000 0.00000
ABNR INTERN> 370.48897 984.70990 200.06852 1085.15295 53.42740
ABNR EXTERN> -182.76891-240659.62365 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

Now( using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 10000-237452.82606 -0.00000 0.00000 0.00000
ABNR INTERN> 13.44942 1160.91816 244.89701 1091.79712 53.47728
ABNR EXTERN> 172.68940-240190.05445 0.00000 0.00000 0.00000


When I used SHAKE BONH PARAM at the post-solvation minimization( set the number 1.0e-9, not previously1.0e-6), the abnormal termination still happened. I felt disappointed very much.I just want to try again and I deleted "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" in inp for equilbirum, then it worked and the abnormal termination didn't happen. So I want to ask: Can I delete this script "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" ? I am afraid for this action. Is this deleting operation harmful for next steps?

Thank you again for your time, my teacher, thank you!

Re: Termination in equilbrium when heating
rmv #37943 06/21/20 02:15 PM
Joined: Jun 2020
Posts: 14
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Thanks,my teacher. Thank you for your suggestions and your time. And this time I tried again and again.

I used SHAKE BONH PARAM at initial minimization before solvation, but I found the energy was higher than previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9 ). So which one is better?

Previous(not using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 3311-238148.54483 -0.00000 0.00000 0.00000
ABNR INTERN> 370.48897 984.70990 200.06852 1085.15295 53.42740
ABNR EXTERN> -182.76891-240659.62365 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

Now( using SHAKE BONH PARAM, shake bonh tolerance 1.0e-9):
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ABNR> 10000-237452.82606 -0.00000 0.00000 0.00000
ABNR INTERN> 13.44942 1160.91816 244.89701 1091.79712 53.47728
ABNR EXTERN> 172.68940-240190.05445 0.00000 0.00000 0.00000


When I used SHAKE BONH PARAM at the post-solvation minimization( set the number 1.0e-9, not previously1.0e-6), the abnormal termination still happened. I felt disappointed very much.I just want to try again and I deleted "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" in inp for equilbirum, then it worked and the abnormal termination didn't happen. So I want to ask: Can I delete this script "shake bonh tolerance 1.0e-9 parameter shake bonh parameter" ? I am afraid for this action. Is this deleting operation harmful for next steps?

Thank you again for your time, my teacher, thank you!

Re: Termination in equilbrium when heating
dengwenhao #37945 06/21/20 05:15 PM
Joined: Sep 2003
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rmv Online Content
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You must use SHAKE BONH PARAM throughout; the errors are caused by other problems, such as the use of CONS FIX instead of harmonic restraints, a possibly corrupted parameter file, and maybe an initial model that isn't very good.

Verify the parameter file, perhaps using a simpler model.

Revise the minimizations to use CONS HARM instead of CONS FIX, and do not apply it to all heavy atoms; just the backbone atoms is likely a better choice. The best choices depend on the source of the model; I would treat a crystal structure differently that one constructed from a software package.


Rick Venable
computational chemist

Re: Termination in equilbrium when heating
rmv #37946 06/22/20 01:46 AM
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Ok,thanks. Though I don't know the reason why we must use SHAKE BONH PARAM throughout, but I believe you are right. At the same time, maybe I know where I should change, I almost forget ask : how do I change the script to achieve the purpose of applying "CONS HARM"(your suggestion) to the backbone atoms instead of all heavy atoms.

This is my old script:
!Make sure no constrains exist
cons fix sele none end

define heavy sele all .and. .not. ( resname TIP3 .or. hydrogen) show end

!Constrain needed locations
cons fix sele heavy end

How do I change my old script, my teacher?

Thank you again for your valuable suggestions. Thank you!

Re: Termination in equilbrium when heating
dengwenhao #37947 06/22/20 02:47 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Online Content
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The CHARMM force field was designed and tested using the SHAKE BONH constraint. The water model in particular is rigid, and requires SHAKE to keep it that way. The PARAM keyword ensures that X-H bonds are constrained to their parameter set values.

Please read the documentation (cons), and look at some the posts in the Script Archive to get some idea of how this is supposed to be done.

Using CONS FIX on all heavy atoms and leaving only the H atoms free to move is an extremely bad idea, indicating either you have received very bad advice, or have not done the proper amount of study yourself before attempting to use this complex program. Make some effort, and show that you have done so.


Rick Venable
computational chemist

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